You can use just about any modeling software to make your own or edit pre-existing weapon animations. I believe EAI uses 3D Studio Max, if I remember correctly. But Blender, Milkshape and Fragmotion all work just the same.
I would suggest starting out by grabbing the Milkshape and Fragmotion trials, importing one of EAI'S weapons, and then following some of the rigging tutorials provided by the community here to get accustomed to the process.
EDIT: Just reread your post and saw that you said you already know how to modify EAI weapons. As far as learning animation goes, your best bet would be to pick a software, and then read up on the animation tutorials for it.
Kravenwolf