I used to be able to teach new spells to followers using UFO. How do I do it with AFT? With UFO you could only teach vanilla spells. I've heard that AFT is a lot more advanced, so can you also teach them modded spells as well? I've got tons of modded spells and it would be great if I could get my followers using them!

I don't know about modded spells (apparently those included in Perxius Maximus won't work with followers), but equip the spell(s) you want to teach your follower and use the tweak options->magic:

By the way, this is covered in the readme.