Well heres what I have been planning to do. I'm keeping the s/c on the inlet side of the motor in about the stock location, about 4cm further down and 3cm farther out to clear the manifold. For efficiency reasonts I am keeping with the draw through setup like it had in the oem setup. You can go blow through, but that would mean the blower is always pumping at max pressure, and sapping enough power from the crank to do so. I'm replacing the throttle body on the tvis intake with just a strait pipe and haveing a flange to mount a tb welded to the inlet pipe of the blower. For simplicity I am going to have the s/c run full time instead of ecu controlled like it was in the oem setup. If i wanted to keep that I would have to rig up a bypass valve from behind the tb to the outlet of the s/c, there is really no loss/gain from not haveing it so I wont bother. As far as running it with a stock ecu the tvis manifold is a bit more efficient then the stock gze is so if you have a map based computer you might run into some problems. You'll probably see slightly less manifold pressure with n/a manifold but the same amount of air will be flowing though. The afm based gze computer should compensate fine, but the map based might be too lean in the fuel map. You might find you'll have to up the fuel pressure, fool it into thinking the air is cooler, or something to richen it up when its in openloop.
Oh here are some shots of it in mock up. Everything is just loose on there right now and s/c is proped in with a piece of wood, but thats how it will eventually look. Wont apply too much to you cause this is a front drive application, but should give the general idea. I painted the s/c blue, don't ask me why, there's a little rice in all of us. So the blue stuff is the sc makes it easier to see. The larger pipe that has a piece of black ruber coupling on it still is the inlet, I'm going to cut it so its at a 45° angle and have a tb flange mounted to it, probably the stock gze tb since it uses a solenoid instead of that stupid wax pellet to control the idle (the #1 cause of bad idles in early 4ag motors). Then the tb will be replaced with a pipe matching the diameter of the s/c outlet pipe. I'll probalby run it with no intercooler for a bit, untill I can get my hands on a jap or maybe aus spec front bumper (more air will flow through that for a front mount cooler then the us spec).