Manual will use a Flywheel bolted to the crank shaft
Automatic will use a Flexplate bolted to the crank shaft
Yes you will need to remove your Flywheel and put it on the other crank shaft, at that time rear main seal can be seen and changed, under $15.
Good pictures here of what you will see: Transmission Swap (FM146 to M5OD) and Complete Clutch Upgrade
I can't remember if there is a spacer between crank and flexplate or crank and flywheel I seem to recall there was one, but can't remember on which one.