Ok, I got the summon Flame Atronach spell and have used it in almost every fight I've been in since I've gotten it, but yet my conjuration skill has not gone up, what's going on?

It levels quite slowly, for some odd reason. I've noticed that myself. If you like, cast Soul Trap on a dead enemy five times for every time you summon an atronach, and you'll level up at a more balanced rate.