With the auto trans, there's a plate that bolts to the crankshaft which the torque converter then bolts to. Make sure you don't use those bolts to secure the flywheel to the crankshaft. Use the ones made for the manual trans flywheel because they are slightly longer than the ones from the auto. Unfortunately, they're easy to mix up if you've tossed all your bolts in one bin but that length difference is important.
I don't know why Saturn just didn't use the longer bolts for both auto and manual in the first place... I suppose they had to save that nickel.
Have fun with your swap. Lane [ lane (at) evilplastic.com ]