Well, sure it works. You have two options:
#1 - create individual map pk3s with the skins. Essentially you repack the map and throw the skins inside.
Please don’t use this option, as it is rather pointless. Nevertheless you should know.
#2 - Throw all your skins in one custom pk3 and put it on the server.
Now depending on which skin (or even model) you want in what map, simply open up the mapscript and enter the respective commands found here.
remapshader "models/players/temperate/axis/engineer/body_engineer.jpg" "models/players/winter/axis/engineer/engineer_body"
Looking at your red star I hope I didn’t fall victim to a troll just now, but anyway, hope it helps.
Cheers