I don't know if it's the template, but I added in a new enemy. It's based on the Imperial Commando, but when I get in game, he doesn't attack me. He walks around and says "Drop your weapon!" and the like. What do I do?

sounds like you used the "post-weapon-force-pulled" template, perhaps. I don't know. I don't have a lot of experience with that.

Yes, maybe what Sarn said. Also, did you fill out all of the fields for the new enemy, including pup, cog, ai, etc. in the quick and dirty template creator? If you didn't feel out part of that, it might be why he won't attack you. If you want more help, I'd recommend you post the model and your template on here.

I filled out all of the fields, except 3do, with the normal Imperial Commando with a rifle. The model is an Urban Commando, part of the allies.zip pack available on Massassi.
Here's my template:
# DESC: Penumbra Soldier
# BBOX: -.04 -.02 -.12 .04 .02 .07
pencom _humanactor size=.123013 movesize=.123013 model3d=urbtroop.3do aiclass=icdefault.ai soundclass=ic.snd puppet=ic.pup cog=actor_ic.cog

did you edit any of the keys?

I find sometimes if I made some keys from scratch, like the enemy fire weapon key, it wont fire at me anymore (or fire strangely).

Make sure you add key event "activate fists" or something.

Apparenty, enemies need a special event data thingy in the fire keyframe for them to fire (in my experience)

if(getThingFlags(source) & 0x8){
  do her}
elseif(getThingFlags(source) & 0x4){
  do other babe}
else{
  do a dude}

I used the standard Imperial Commando keys, so I have no idea what to do.

Try making the parent template the commando instead (template name 'icommando'). It looks like your template is missing a lot of flags and stuff defined/set in the commando template and not in the _humanactor one (ai, for example)