Derik, characters are done the same way. In my experience, chracters are a little more difficult to rig than weapons. Regardless, the process is pretty much the same.
You only modify the .fpi files after you have rigged the entity.
As far as difficulty and learning. It can't be made much clearer:
1: Convert both your old and new models to the Milkshape format.
2: Open the model you want to Rig into milkshape. Click the "Materials" tab and assign your textures.
3: Then click "File" and click "Merge" and open a weapon that has an animation you want to use. (For example if you wanted to rig up an assualt rifle, you could use the commando)
4: Double-click the Group(s) for your new model. (This highlights it in red)
5: Use the "Move," "Rotate," and "Scale" functions located on the "Model" tab by clicking one of the function buttons and moving your mouse to adjust the highlighted weapon. Position the new weapon so that it is in the same location in Milkshape as the animated model.
6

ouble-click the Group(s) again to deselect your New model and then double-click the animated model to select it.
7

nce the animated model is highligted press the Delete key. This will remove the model but leave the animations.
8: Select an group item such as "Magazine" to highlight only the magazine in red, then click the "Joints" tab. Find the "Magazine" joint and single-click to highlight it. Click the "Assign" button to assign the joint.
Repeat step 8 until everything has been rigged.