I'm going to answer your second question first, since that's a common beginner mistake.

When you first colonize a planet, you're a small occupation force, and occupation forces are expensive (that's not really canon, that's just how I envision it).  What you need to do in order to fix this is to purchase population planetary upgrades for your planet.  These increase the maximum population of the planet and remove that natsy planet upkeep.  One upgrade will remove upkeep from asteroids, but full-sized planets require two to remove upkeep completely.

Refineries are a nifty way to increase your metal and crystal income.  When you build them, a refinery will automatically dispatch worker ships to every resource extractor within a 1-jump distance from where you built the refinery, and will give you extra income for reach extractor it affects.  However, this bonus caps out, and no more than three refineries can service the same extractor.  One of the upsides of refineries is that they are unaffected by loyalty, so they work well in larger empires.  In most situations, building trade ports and buying metal/crystal on the black market with the proceeds is an easier way to generate cash, but sometimes there are good locations to build refineries.

https://www.sinsofasolarempire.wikia.com/wiki/Planetary_Improvements

If it's on the front lines, yes it can be shot down, and the enemy will capture a small amount of resources from it.  The refinery will take 30 seconds or so to replace it, during which time you lose the extra benefits from the extractor it was servicing.

Refineries increase the income of extractors; you need to have the extractors already built for refineries to have any effect.  IIRC, you get an extra 0.08 resource income from each extractor per refinery.

Yes, the "develop planet" button is the right button to press.  This will bring up the menu of planetary upgrades.  There are a variety of upgrades available; some increase the number of structures that can be built around the planet, one increases the difficulty of bombarding the planet, and one increases the planet's maximum population.  You don't need to research anything, planetary upgrades are always available.  They are a bit expensive, though.

Heheheh... I wrote a fair chunk of that article

Generally you don't want to max out population upgrades right away (since that's expensive), but instead purchase just enough to get yourself out of upkeep.  That's one upgrade for an asteroid, and two for other types of planets.

OK thanks, I think I get it now. I thought that the number in red - that is the amount of money that the planet costs me - was actually the amount that the colony made me, so when I saw it go down when hovering over the upgrade I thought it was a poor upgrade.

So when I have two planets in a line, then a wormhole, then another planet, can I get a trade route there or will this not work because the line is broken? I am unsure what it is called, but these trade goods freighters... Check the screenshot. Note that I have two planets linked, then another planet that is seperated from the rest by a wormhole. Can I get these good-routes up here? Any tips in general for when to get these goods freighters up?

Thnx.

One more then since you guys are so helpful. I destroyed the cap ship of one tool of an enemy and then I managed to to grab the vulcano planet next to his capitol planet. I defended it with a starbase. In between my home worlds and this vulcona planet is this asteriod field that has enemy extractors on the metal-extractors. For some reason my ships won't destroy them yet I hovered next to them - and I had a colony vessel there as well - and suddenly I captured one of the extractors.

What is the deciding factor in capturing these neutral extactors? I can't seem to find out how to grab them.

Thanks for the replies. I got the advent on a random and I clearly have no clue what I am doing.

On another note, how can I send fleets to other star systems? I looked all over the tech tree but I spot no tech that may allow me to send ships to my allies.

cant give ships away (even with Diplomacy )

research farjump or something like that its a tier 3 or 4 (needs three for four civilian research modules) research

So what is the deal with these trade routes? In the screeny you see three of my planets. I got trade docks there, and then a starbase as suggested in the black hole spot. The starbase got the merchant docks upgrade (yay I remembered a name). I did this before I saw the advice not to do it. Anyway, when I now hover over my credit income I see no white line. Did I do something wrong? 

Even though he's built a loop, he should still have a trade route.  The fact that the trade route indicator has completely disappeared is odd.  The starbase itself will only shorten his maximum trade route by 1 jump (at least as far as I can see in this screenshot).

Imagine a hypothetical trader; he will always search for the shortest path between point A and point B, but will only travel between planets with trade ports.  The most distant two points in your trade network form your "longest trade route".  If you build a shortcut you could end up making two distant locations connected much more easily, and that shortens your trade chain.

First a disclaimer:  I can only see the planets in that screenshot, so it's always possible that you could work with the other planets I cannot see to produce longer trade chains.  Secondly, I was wrong before; you actually lose two links in your trade chain with that starbase.

If you didn't have the starbase trade port on the wormhole, this is your longest trade route:

Homeworld - Ice (near) - Asteroid1 - Asteroid2 - Asteroid3 - Ice (far)

The homeworld is essentially a "dead end".  It's as if the wormhole doesn't even exist, because there's no trade port there.  It connects to the ice, which connects to the three asteroids, which leads to the distant ice.  This gives you a 6-link trade route (sometimes called 5-jump trade route).  Even though the terran planet and the far ice planet are actually very closeby, the wormhole doesn't have a trade port, so it's as if they aren't connected at all.  When you add the wormhole trade port, you've created an open loop (so there are dozens of possible trade routes totaling 4 links).  Here is one possible trade route:

Ice (near) - Homeworld - Wormhole - Ice (far)

Even though the far ice is connected to asteroid #3 (the one on the far right), the trade route cannot extend there.  The reason is that there is a faster short-cut to asteroid #3:

Ice (near) - Asteroid1 - Asteroid2 - Asteroid3

Similarly, because there is a shortcut to the far ice, this potential trade route also cannot be extended.  In order to force the trade route to extend, you must close one of your shortcuts by scuttling a trade port.  You have two options.  The first is to scuttle the starbase (probably don't want to do that; that thing is expensive), but the second is to scuttle the trade port on asteroid #1 (the one on the far left).  This would close the second short cut, and allow the following trade route to exist:

Ice (near) - Homeworld - Wormhole - Ice (far) - Asteroid3 - Asteroid2

Because Asteroid1 has no trade port anymore, it is as if it doesn't exist for the purposes of longest trade route.

Then you didn't create a loop.  As I said, your trade route shouldn't have disappeared entirely (even if you did create a loop) so something is up here.

The ships themselves end up in all sorts of places.  I've seen them get way off course.  So long as they don't get themselves blasted (which will result in a temporary penalty to their parent trade port) the physical trade ships actually haave no impact on trade income and are more or less just random noise.

If you develop wormhole travel, you'd still need a starbase with trade port upgrades on both sides to make a connection, and even then that might not connect to anywhere in particular and have no effect on your trade route.

A refinery affects all extractors in its own gravity well and in each adjacent gravity well.  Take the following example:

A = B = C
     ||    ||
      D = E

If you put a refinery on planet B, it will affect all extractors on planets A, B, C, and D, since they are all connected by phase jumps.  Similarly a refinery on planet D will affect planets B, D, and E.  In other words, the more phase lanes leading out of a planet, the better it is to place a refinery.

Refineries benefit all extractors in each gravity well they affect, but each gravity well can only benefit from three refineries.  For instance, if you built two refineries on each of planet B and D, then these planets would only gain the benefit of three refineries.  Even though there are four refineries in range, they cap out at the benefit of three.

Basically, if you're putting refineries on multiple planets, you're going to run into stacking issues.  Even if it's only every third or fourth planet, you will inevitably get some overlap.  Combined with the high cost of refineries, this is why most people use them sparingly and prefer trade ports.