Mapping for such mods can be done just as mapping for HL or CS, but it's a lot easier when you can get a hold of an appropriate .fgd file for that mod. Otherwise you're going to have a hard time finding out what new entities are used in that mod. But all the basics still apply.
You don't need to place a level in the .pak files in order to work bytheway. Just place them in the modname/maps folder and you should be able to play them. To get lighting to work, be sure to have at least 1 light (or any other light emitting entity or texture light) in your level, and make sure there's no leaks.
EDIT: Enemies are just entities like monster_grunt or monster_alien_slave and the like.