It's really fairly simple, but easiest to do if you are making the level for both games simultaneously. Test and restest to be sure it works. There is no real "conversion utility" and simply saving the Gob file as a Goo will not automatically convert everything. It takes some time, more or less depending on the level.
MOTS contains many textures that are different from those in JK, and MOTS textures should not appear in JK levels as a rule. However, the rest can easily be converted in any JK editor (JKEdit, JED). Also weapons are different and are balanced differently. The personalities have different abilities, so you have to keep this in mind when converting levels. Many JK levels will not make good MOTS levels without some reworking and adjustment. Changes should also be made to take advantage of the advanced engine features like colored lighting.
If you are asking simply about making some JK levels for MOTS, keep in mind that all of the MP levels that came with JK (the 6 deathmatch and 3 CTF) have been converted to MOTS already.
See Hedge's "MOTS CTF" (a very good conversion) http://www.jediknight.net/ctf/
and MERC_Tiberius's "JK2MOTS (the best one I've seen yet)." www.jediknight.net/kicker/