JASII, let me use an LTR system used in the Milwaukee area as an example. This is a General Communications LTR system in Muskego, Wisconsin.
01 451.5500 home channel for 0-01-... talkgroup id's
02 451.7500 home channel for 0-02-... talkgroup id's
04 452.2500 backup frequency for all TGID's
05 452.1750 home channel for 0-05-... talkgroup id's
08 461.8250 backup frequency for all TGID's
The 996 will find the an LTR frequency doing a custom search set to control channel only. A system user has to be talking at the time for it to work. If the talkgroup shows 0-01-015 for the frequency, the correct LCN is 01. The only trouble is that all the home channel talkgroups (01, 02, and 05) can use all the frequencies in the system at any given time. While still in custom search, you can hold on the frequency and wait for the 253 identafier to come up. This always shows the correct LCN for the frequency, but this can take a little time.
The other way is like you pointed out. Set up twenty systems for LCN's one through twenty. Label each system as LCN1, LCN2, etc., using one frequency at a time.
As you find LCN's for the frequencies, set up the system and see if it works. There is no simple way to do this. It takes time.