Only use it once outside, doesn't seem to work during the tutorial, didn't for me.
Only give yourself enough EXP to breach the next level requirement.
If you give yourself too much EXP you will still only go up one level at a time, but you might jump a few levels, which happened to me, and still only get ability and skill points for one level.
The EXP option does work.
in the perm trainer, we will enable adding the ability and skill points at the ESC screen so you wont have to wait until you actually have 'LEVEL UP' showing to add more points.