(I'm guessing Impulse keeps it up to date automatically)
If you installed via Impulse, you were automatically patched to the most recent version during installation. If there are patches in the future, you will be alerted via impulse and can patch from there, but it will not automatically patch without your permission.
I had some newly researched missile frigates being build (JAV I think they're called). 8 of the buggers
Eight frigates is not a particularly large fleet. In fact, that's quite a tiny fleet. On the random-small map, I'd typically want to have 20-30 of them for my initial push against the enemy.
I send them in just after my cap ship explodes
Sounds like the battle was already a lost cause and you needed to retreat much earlier. Remember that Sins is a relatively slow-paced game, and that means it will take a while to retreat. You need to think ahead and start your withdrawal before your capital ship has taken serious damage.
I think I'm just having balance issues and don't seem to be able to balance my expansion against my research...I don't think I'm doing things quick enough either.
It's very common for people to spend too much on technology. Unless you're playing on "fastest", you really don't have any business researching anything except unit prototypes and ice/volcanic colonization in the early-game and should be diverting all your cash towards military units and colonization. Later on tech becomes very important (and on the faster game speeds it can pay off sooner) but early-game on lower game-speeds you need to prioritize military and expansion to the exclusion of everything else.
If you want specific pointers, you can post a replay and I'll critique it for you.
The other three capitals are pretty much unheard of as starting capitals.
The Vasari Kortul is a suitable battleship, also the Marza and Vulkoras dreadnaught class capital ships are also viable (but only in the hands of master). Kol, Dunov, Rapture, Revelation, Radiance, and Antorak however are indeed unheard-of as openers among experienced players.