How can I put my skin in game?
My custom skin is in base/models/players/stormtrooper.
In the stormtrooper folder there is:-

animevents.cfg
model.glm
sounds.cfg
Jicon_officer.jpg
Jshoulder.jpg
Jhelmet.jpg
Jmodel_default_officer.skin
armor_spec.jpg
torso_legs.jpg
torso_legs_spec.jpg

I then created a SKINS folder in my gamedata folder and copied the model folder and everything inside it, into the SKINS folder.
I then go into the SKINS folder and create a .zip file. I double click that and click add. I add everything from the SKIN folder into the .zip file, add all subfolders is ticked, and I press "add with wildcards".
I exit winzip and rename the .zip file into a .pk3 file. I put it in my base folder and run Jedi Academy but my skin does not appear in profile.

Does anyone know what I am doing wrong?

You need to turn on the retain directory structure.