Welcome to the forum and the mod.
We get this question from time to time.
The major differance is that the AST (Atrocities Star Trek Mod) use standard Space Empires IV technology with some racial trait specific weapons and stuff. It is basically SEIV with a slight star trek flavor.
STM (Star Trek Mod) is a complete conVersion mod that use exclusive star trek technology and racial traits.
Both mods are good mods, but for the best Star Trek feel, I recommend the STM v 1.7.5.
EDIT:
Since your new I should also point out that you will need to download and install the Image Mod files. These files are required by the both the STM and AST mods.
www.spaceempires.net IMAGE MOD MIRROR.
These image mods include Planet Pack, Facility Pack, Component Pack, Combat Pack. You install these over your exsisting Space Empires IV / Pictures / ABOVE NAMES folders. They will add extra content to each of the folders, more planets, more facilities, more components, and more combat images. They will require that you over right ONE file each. Planets.bmp, components.bmp, facilities.bmp, and combat.bmp.
The reason for this is these bmp's are the mini images that are used in the game, and therefore must be included for the game to use them correctly.
Also you migt get an error over missing system image. Usually Nebula5 or something. If you do post and we will tell you have to fix this. Its easy to do, but requires that you download the FQM Delux mod and copying over some images into your STM folder. Fyron can explain this better but I think by the time that this happens to you, you will know how to do it yourself.
Also UPDATE to the latest Version of Space Empires IV. (1.91) This is critical. Have fun and good luck.
[ August 03, 2004, 00:03: Message edited by: Atrocities ]