OK, so the 'right' way to play AI war from everything I've seen and read is to keep AIP to an absolute minimum and planet-hop your way to victory.
First and foremost, AI War is not a game with one way to play. In fact, there is no Arcen's game I know where there is only way to play. So floored AIP and archipelago empire is
one way.
That doesn't work for me.
Then find your way. If you are comfortable with 400 AIP and a big powerful fully-connected empire, it's fine. And maybe with this way you would be able to deepstrike and handle threat more easily.
But to answer more specifically to your question, how to manage a low AIP / archipelago empire? The way I do (and there could be many way to walk along a way) is to defend remote systems, this way I would spare the knowledge for MkIII engineers (I unlock them only on Fallen Spire campaign, when HabCenter's + exo scrap metal skyrocket above what I can spend with all my engineers on mercenary space dock). You use SpireCrafts? If you take the hard version, maybe a high AIP style of play would suit it best. Low AIP / archipelago stands no exo. So I take remote systems (usually the ones with A-prime CSG), defend them with full caps of MkI turrets, and move my fleet away to continue the mission. With <100 AIP (on 7/7 diff, I mean), waves are handled by MkI turrets. And with 150.000 energy per PGen, each remote planet can supply all the MkI turrets with a little extra for your fleet.
Then I use my HaP to get some more designs, use K on fleet/starships and go for the homes once all CSG are down. And that's how I handle a 7/7 vanilla low-AIP game. And as I say, this is only one way. (But it's always fun to go out of the comfort zone and challenge oneself)
Hope it helped.