First of all, DOHC means SL2.
Next, I can tell you for sure that even with one being an auto and the other being a manual, YES, you can just take out the flex plate (that's what it's called on an auto) and put the flywheel from the manual in it's place. No harm done there.
Also you must realize that you're going from a second gen engine to a first gen engine. The basics like the block, head, and engine mounts are all in the same place. If you were trying to put a 91 engine in there, I can tell you that WON'T fit. The wiring harness is going to be a pain to swap out because:
1. You're trying to put an auto engine in a manual car.
2. First gen was OBD-I, whereas IIRC, second gen is OBD-II
Furthermore, your cam cover will be different on the donor engine. That shouldn't be a problem though. You MAY have to fabricate a way to connect the PCV valve to the donor cam cover, as the vaccuum hose length is different, and the PCV valve itself is positioned in the cam cover at a different angle (I'm pretty sure on that one... working from memory here), then again that may only be a difference between the coupes and sedans.
Lastly, there is one thing you are definitely going to want to do and that's pull the engine AND the transaxle at the SAME TIME, otherwise, you're going to be in for a major PITA when trying to put the donor engine back in the engine bay. Some say it's easier to drop the engine out the bottom of the car... yet still others say it's best to take the hood off and just pull the engine/transaxle as one unit.
I think you are better off to keep shopping for the same year engine but if you REALLY wan't to try the 92 engine:
You can find some really nice walkthoughs on
www.saturnfans.com and there are even some external links there as well. If this is your first time pulling an engine, take your time and do it right the first time. It's a true morale killer to swap an engine on your first try, then turn the key and nothing happens.