I don't have a copy of Fragmotion or Milkshape (or FPSC) on this machine, so the steps might be a bit vague, but here we go:
1) Find the HUD.x file of the weapon you're modifying. It will be in gamecore\guns\
2) Open it in Fragmotion.
3) Export it as a .ms3d file with the animatons included.
4) Open the .ms3d file in Milkshape.
5) Merge this with your silencer which is ideally in another .ms3d file.
6) Apply the appropriate textures in Milkshape. The texture for the silencer should also be placed in the folder with the HUD.x file and this be the path specified.
7) Assign the silencer model to the main gun bone. It may take some time to find out which bone is the appropriate one as different modellers name their bones differently, but you can usually tell which is which by testing the animations and if the silencer remains attached to the gun, it's corrrectly assigned.
8) Re-save the model as a .ms3d.
9) Open the .ms3d in Fragmotion.
10) Back-up your original HUD.x (save it as HUD.x.backup, or whatever suits you)
11) Export the model from fragmotion, making sure the animations and textures are all applied as the new HUD.x.
12) Delete the HUD.dbo file from the directory (assuming it exists).
13) Test it in game.
Like I said, I'm a bit rusty with weapons as I haven't done it for 6 months and FPSC doesn't work on this laptop, so all the steps are done from memory, although they're all roughly correct. I'm also assuming you have a basic working knowledge of Milkshape and Fragmotion (you of course, having bought them, and to not know how to work them would be a serious case of "all the gear, no idea".)
I'm sure someone better versed in weapon modification can help you further.
