If you want every Unit to use those animations, just put the anim files to BF2_ModTools\data_###\Sides\Common\munged and munge your sides.


If you want only one Unit to use it, change in munge.bat the red marked thing
to something else, example:
and start the munge.bat.

Now put your human_prone.anims,human_prone.zaabin and human_prone.zafbin to BF2_ModTools\data_###\Sides\Common\munged

---Not sure about the following Part---

Lets say you want only your EP3 Clone Sniper to use the anim.

Go to BF2_ModTools\data_###\sides\rep\odf\rep_inf_ep3_sniper.odf

and put this line at the bottom of the file:
Now munge your sides.

---Not sure about the Part above---

how do you make your files in to a zaf and zaa files...

Your anims, zaabin and zafbin files are created after you started the munge.bat. Not sure in which folder, I think in BF2_ModTools\assets\common\MUNGED. Just use the windows search function.