I think you'd be better to post this topic in the http://www.kerkythea.net/joomla/ website. Have you already tried a test render to KT using KT2SKUP? It determines the path on the first run. If you do have problems with KT, I can recommend stumping up for Twilight Render - it's very straight forward to use for SKUP users while retaining the power of Kerkythea. Best of luck!

OK then, you have two choices. Wait till someone more knowledgeable at Kerky than me chimes in here - or go to the KT Forums and (hopefully) get a more prompt but even more importantly; precise answer there.