Hi there smogover,
You save the mods or patches to a seperate folder from the game -*don't* save them into the SH3 DIR!!
Some mods either have an actual installer -you point it to your SH3 DIR, or when you extract the mod in a .zip/.rar format -to a temp DIR usualy- you will see it may have subfolders containing names the same as the subfolders in SH3.
You can then copy the .tga files or folder into the same relevant folder in SH3 and that's it!
Official patches from UBI can be run from wherever you save them to, ie 'SH3 Official Patches' folder that you make previously. It will automaticaly find your SH3 DIR through the windows reg.
Most complicated mods come with a readme.
Back up a folder(s) that your copying stuff into, in case it writes over the original files and you want to return the game back to the original.
Have fun!