I am trying to make a mod that will replace all the clones with re skinned versions of the regular phase 1 clone trooper. I have no Idea where to start and would like some help. Thank you.

Then you would be wanting to make a custom side. It would be a simple .odf edit (with notepad) to change the model of the soldier, and a .tga file edit for the skin (open with gimp save with compression off). Read the documentation that came with the mod tools, if you have other questions the everything you need thread (stickied) should cover it.

This might be helpful: http://www.gametoast.com/viewtopic.php?f=27&t=12729

To edit an existing side go to assets -> sides and copy the side's folder and Common.
The folders are:
all - Rebel Alliance
rep - Republic
cis - Separatists
Common - Common files always copy this or else your sides won't work!
des - Jawas and Tusken Raiders
ewk - Ewoks
gam - Gamorrean Guards
gar - Naboo and Temple Guards
geo - Geonosians
gun - Gungans
imp - Empire (Imperials)
jed - Generic Jedi
snw - Wampas
tur - Turrets
wok - Wookiees