The Mannequin view should include the following panels. Fragments (left) Fragment Editor (top middle) Timeline (bottom middle) Anim Clip Properties (right bottom)
The Fragments panel holds all your animation ID's. This where all you animation's/fragments will live.
At the bottom you'll see 6 buttons...the top row is related to fragments the second is the ID's.
Click the "New ID..." (shown above). You'll get a new window "New FragmentID Name" add the name you require and press ok,a follow up pop up will appear, where you'll see the options below, with tick boxes for the scopes you can choose from.
Select the newly created ID and click "New" (above the "new ID" button) and this will insert an new fragment "<default>" under the folder selected.
Double click the new fragment created and you will see the new file created displayed on the "Fragment Editor" timeline
This is where the magic happens...the animation setup will be done here.
Right click on the "Torso1P" scope ----> Add Track ----> AnimLayer
This will create a new animation layer for you to use.
Double click at the start of the new layer created (demonstrated in the image below) to create a new blank key.
Select the key you just created and head over to the "Anim Clip Properties" box to the right.
On the first line "Animation" you'll find an option box to the right, click it and this will open the "Animation Browser"
The animation browser is pretty much like the Character editor, a place where you can find all the animation in game. Search for the animation, you'd like to add,(Filter search box) and double click it. This will add the animation selected to the newly created animation clip.
To the bottom left of the Fragment editor you'll find options that you can add to your newly created fragment.
Say for example your fragment contains the M9 weapon, and the stance is ironsight...you go to the "weapon" option box and select M9, and on the "zoom" option you'd select "Iron".
This in turn will change the name of your fragment from "<default>" to "m9+iron", this is what the tag the coders will need to insert in order to work ok in game.
Save your file: File ---> Save Changes ----> Check Out Selected Files -----> Save
If you finish adding fragments, head over to perforce, and check in the file you've just checked out with Mannequin.