Well, you have to have JK to use MotS, so you've lost me. It's a simple case of re-naming the skin 3do to kk.3do and km.3do, and placing all the relevant .mats and 3dos in the right directory (MotS\Resource\3do and resource\3do\mat) I think - I forget. I usually just .goo the files myself and use it in Patch comm.
Since MOTS uses the same file format, it should be simply a matter (of as above) changing the name. Of course that only applies if you use them in SP.
kk.3do is the default for SP in MOTS (at least for the levels with Kyle in them). However ky.3do is still available, so even if you don't change it, it will just replace the Kyle Katarn skin (where he wears his JK garb).
If the skins use any JK specific textures, make sure you change those too.
JK Skins to MOTS
Hybrid Mode
