I would say it's more time consumeing than hard to do.
First you will need a computer from a Manual car, then the entire tranny w/ clutch cables, shifter ect.
The tranny will bolt right up to the block no problem. The worst thing I think will be getting a clutch pedal installed! The shifter and cables should be no problem!
AND BTW you can expect a few more HP from it being an MTX than an ATX.
Good luck! OH and you might want to look on Neons.org or Allpar.com for a how to on the tranny swap. Good luck!