build after coming up with an idea. it doesn't have to be a complete idea, you just have to know the general direction you're headed.
set goals for your build.
regen/output really is just numbers, and the larger you can get the one you're focusing on without crippling other systems, the better. usually i focus on shield capacity and recharge with just enough energy to keep recharge at full and fire my weapons at the same time.
taking on much larger projects is just the two points above combined.
order of which you build ships really depends on your idea. start building whatever you need to get a framework to build your idea from, and after that it really doesn't matter what you do first. i constantly alternate between interior, exterior, and systems, making changes as the ship develops. kind of like how an organic living thing grows from a basic form to a completed adult form.