Roman,
The LightJet should have a PC hooked to it via a SCSI cable and running a program called LJFE or LightJet Front End. This software/PC combo combined with a densitometer are used to calibrate the loaded paper and processor chemistry.
Usually, a 3rd party rip like PosterShop is used to submit files to the LJFE. If that's the case, then profiling should done through them.
Without a rip, the LJFE just transfers RGB tiff data to the 5000 and does nothing with profiles. This can be a good thing...no convoluted rip screening algorithms to complicate the issue. Once your media is calibrated, treat this as an RGB output device. First generate Linearization patches in Monaco or PM5 and save them out as a tif file then transfer that to the LJFE. Once that has been processed and read, you can follow it with the profile patches.
After you create your profile, you will need to do all color management (profile conversions) in PhotoShop. Essentially you want to convert your image to the output profile before you fine tune your color and submit it to the LJFE for printing. I suggest giving it a different name so you don't overwrite your master file.
check out
www.cymbolic.com and
www.oceusa.com for more info.
-Mike