Well, your early build order seems good, so I'll just answer your specific questions. The "white line" represents your longest chain of planets with trade ports that only goes through each planet once (basically it will only be a line, you won't get closed shapes). It's a little weird how it decides that chain, but once you get the hang of it its a good way to increase wealth because the amount of credits you get from each trade port increases with each planet you add to the chain (even if they are on planets that are not on the chain). Thus an empire with eight planets in a line with a trade port on each will get more income than an empire with 4 four planets in a line with two trade ports on each planet even though the number of trade ports are the same thanks to the chain bonus.

Refineries give additional resources based on the number and type of resource asteroids in the gravity well they are in as well as in adjacent gravity wells. This includes extractors in uncolonizable gravity wells that you control, and as a general rule of thumb 8 extractors have to be effected for them to be worth while. If you have a long trade chain you will need 10-12 to beat out the usefulness of a trade port, so they are used far less frequently.

I don't really know what you mean by level up population bonuses, but if you mean upgrading the population of each planet, in general you just need to get the development rate out of the negatives (the first upgrade for asteroids and the first two for everything else). Then you just need to upgrade it once the population cap is reached (if you think you can hold the planet of course).

If you know you can hold the planet and will be to busy to go back and check the population cap, then getting all the development upgrades at once isn't a bad thing. It is just getting rid of the underdevelopment penalty (that causes the negative credit value of planets early on) that you at least have to do. Increasing it beyond that point (after the second upgrade) just increases the max population but does not increase the population growth rate. So the later upgrades don't help until after the current population cap is reached.

You've got the refineries right, but any planet with logistical slots can have a "viable trade route". Even if it doesn't increase the trade chain it will still generate the same amount of credits as every other trade port in your empire without planetary bonuses (unless your trade ships try to go through an enemy planet and get destroyed quickly). The bonus from a long trade chain is applied globally to every trade port in your empire (which is why extending it can bring generous payoffs), so even if that planet is in a completely different solar system, it will generate the same amount of credits as a trade port on your homeworld that is in the middle of the trade chain, because both gain the credit bonus from that trade chain.

Also, I should mention that early game the best method expanding your economy is to simply get as many planets as possible. Plenty of people have run the numbers and acquiring planets, building extractors and getting the early population upgrades are by far the most cost effective way of increasing your income. The fact that your research base and ship production are also somewhat based on the number of planets you control make this even more vital. Do not start investing in trade ports or anything else until you can no longer expand to neutral planets (or enemy ones if they are lightly defended).