1. Open the .md2 for the weapon you want to add to your model in Q2modeller (i.e. w_rlauncher.md2).
2. Go to File>Choose Reference Model and open the tris.md2 of your player model.
3. Go to File>Merge and open the weapon.md2 that was animated with the tris.
4. Press the "Face" button to go into face mode, go to the edit menu and choose "Select Inverse".
5. Move and rotate the new weapon until the handle is in the same spot as the original and the barrels point in the same direction.
6. Save your work here as an .AQM to save yourself from a lot of frustration.
7. Click the vertex button to go into vertex mode and select 4 vertices of the model's weapon.md2. Try to select 4 verts that are in a plane parralel to the alignment of the new weapon. Also the verts should be spread far apart, for example, try choosing two on the tip of the barrel and two on the butt of the gun.
8. Go to the "B" tab and click align. Move the animation bar to see if it aligned right. Many times it won't and the weapon will fly all over the place. When this happens, you have to try it again. So go to the file menu and open the .AQM file you saved (you can't undo align) and go back to step 7.
9. Hit the face button to go back into face mode. Go to the edit menu and choose "Select Inverse". Delete the original weapon and export to .md2 and you'll have your new vwep model. You will also need to "link" the new weapon.md2 to the weapon skin, but that's not being covered in this tutorial...