erm, I'm not sure I've understand that sentence...
Generally to alter things, figure out which structure it's in, under structures tab, use 'Write ms3d File-incl damaged' edit in milkshape and replace using 'Replace with ms3d File' selecting the same structure.
If you're only just starting doing this I recommend
use Blender instead!
Blender is free and can load the whole .world at one time which makes things much easier...
Rules for both are similar, if you leave the names of objects/groups the same and just tweak the shape/uv then you shouldn't need to do much else, and IWTE will retain the existing characteristics like collisions and firing slots - but bear in mind if you change something that has an animation, you'd either need to change that too, or they won't match.