You should be able to simply place the tga files in your resoruces_override directory and start the game (make the appropriate textures\...\ subfolders for this! certain folders cause different conversion options to be used (tints, )

If it doesn't automatically create a textures_agh\...\file.agh for each textures\...\file.tga then here are a few things you might try:

/setpref updateAGHFiles true

and then restart or use /purgetextures

(you'll need this in your commands def in resources_override)
Code:
		//purgeTextures
		{
			string name = "purgeTextures"
			string abbrev = "purgeTex"
			string usage = "[no parameters]"
			string description = "Purges all texture and image resources for immediate reloading."
		}
I'll test this out myself later after work.