@taixzo
Do you really need 2 nitdroid entries selectable in menu? Then proceed as coderus said.

I also have two nitdroid instances, but have to do a command line one-liner on harmattan before booting up (as I normally know which instance I want).
I have two nitdroid folders named nit_ics and nit_jelly. Furthermore one link named nitdroid (the one mentioned in preinit_nitdroid) pointing to one of those two folders.
Easy peasy.