The shaft with the splines on the transmission is known as an Input Shaft..
Axles are the shafts that come out of the transmission and drive the wheels... Just wanted to help you out with your part names.
The input shaft is supported by bearings etc and it would take a LOT of force to do any damage to it so I'm sure your fine.
There are holes in the pressure plate that sit on dowel pins on the flywheel. They are offset so it will only fit one way. Be sure to use an alignment tool when installing the clutch so that the input shaft will slide threw and in to the pilot bearing with out a lot of effort.
Also don't forget to use locktight when installing the flywheel bolts. You should also put in a new throw out bearing as well. They are about $35-40 and it sucks when you swap everything out and then it goes bad a few thousand miles down the road.