The only real advantage to using a dedicated gfx solution for something like what you're mentioning is when 3d comes into the equation. That said however the heaviest 3d games available for 68k amiga are things like quake, quake2, descent:freespace, payback, Cube, tux racer, etc. so requirements arent huge anyway. You will get higher framerates with a dedicated card, but even a cheap nasty 2nd hand $10 geforce, radeon, etc card will suffice (Quarktex will let amiga os access hardware acceleration of the hardware its running on via warp3d).
As for setting up amiga os from scratch rather than using one of the prepackaged "distros", in my opinion it's the way to go and how Ive always done things. This of course is all down to personal tastes and there's no harm in using amikit/amigasys/etc., but personally I like to know the system inside out, and it's much easier to do that when you've installed everthing yourself. As for which Amiga OS to use, I guess that's up to the user, but os3.5/3.9 being a little slower than earlier versions of os3.x doesnt matter too much when the resources available to an emulator are on offer.
