thats easy...
ok if you read that section of the manual, it tells you that you should download a really cool program called ifranview. that program reads the dds files for the original entities. i dont know if you know this, but when you run a game, fpsc creates dds files from tga files...so lets say you wanted to re-texture a weapon...ok thats easy,
first, you open up gun_d2.dds (using ifranview), thats the default texture for any gun. then you can convert this dds file into a bitmap or anything, so you go to "save as" and select BMP (or whatever)and select your path name, the open the pic up in a 2d editing program (such as photoshop or image ready) and change it as you see fit...then just export it to the entities original folder as a TGA and delete "gun_d2.dds"
IMPORTANT
makesure you have backups of all the files you delete!
hope this helps
-BULLSHOCK
-I will beat anyone in HALO2!