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.