ace here is a place you can learn all you need to, maybe not all,about milkshape.
http://www.make-video-games.com/milkshape/milkshape-tutorial1a.htm
Also, if you goto "docs" in you fpsc file you should have a manual from fpsc foums called "FPS Creator Help.pdf" in which wetham shows how to animate a weapon using milkshape.
Without an explaination of what you are trying to do I cannot help. The pic showed two joints attached to each other. If you were trying to make the box move up and down do this:

add new joint,go to the "joints" tab and name it "Main or Body", then unselect it

add another joint just slightly above "Main or Body", name it "bone1"

while you still have the "bone1" selected, add a new joint, just slightly above "bone1", now name it "box", now you should have three joints, two which are connected and one by itself

now you will need your box for this step, you might need to create one if you haven't already. go to the "joints" tab and select the joint name "box", now go to the "groups" tab and select your box, go back to the "joints" tab and press the "Assign" button. this assigns the box to the "box" joint.

with that done click on "Anim" at the bottom, now set the frames to 30 in the last two boxes, now in the box that is blank put a 1 in there

now goto the "models" tab, press "select", then in the select options menu press "joint" this will allow you just to move only the joints

now press "Ctrl+K" to set the first keyframe

now move the slider to 30, or simply change the 1 to 30

with the joint named "box" selected move it up to where ever you like and press "Ctrl+K" again to set the final frame. to see your animation press the the play button or the one that looks like this ">", you should see the box moving up and down. Congrats you made a box move up and down
I hope this helps you and others. Sorry no screenies, but that takes to long for me.