First of all, you will need pakscape and a photoshop or paintshop pro (or something the like)
Open pak2.pk3 with pakscape. (or a zip program). with pacskape, click the textures folder, models, and weapon folder. Now choose which weapon you want to repaint, open the file in photoshop or whatever,
then it up to you how the weapon are gonna look like, anyway, when you have done that, save it as a tga file, for example, colt45.tga (include .tga in the name)
then go to pakscape, click the "new" button in the left corner, then make a folder named textures, then a folder named models, then a folder named weapons, and then a folder named "weaponsname" (for example, if you're repainting a colt45 skin, name the folder to colt45.
Then put the colt45.tga file in your colt45 folder, and "SAVE AS", save it as a pk3 file, and name the file to user-colt45_pistol.pk3.
Then put the pk3 file in the "main" folder to mohaa.
That should do it. That was kind a fast guide, if you wanna know more, read the guides at alliedassault.com
http://www.alliedassault.com/community/guides/