There is no rule for this -- simply put, by trial and error. LCNs and corresponding frequencies are programmed into the radios, the control channel emits only the LCN and not any frequency equivalency information like for P25 systems. LCNs do not even have to be created without gaps -- theoretically a system may use LCNs 03, 07, 08, 12, 14.
If you program in the control channel, many scanners will display what its LCN is. If the control channel regularly changes frequencies then patiently monitor and you'll eventually accumulate data that way.
It's much easier and quicker if you have something like Unitrunker running plus another scanner monitoring the repeater frequencies conventionally. You can correlate Unitrunker-displayed activity for a particular as-yet-unidentified LCN with activity on a frequency.
Systems often have LCNs assigned sequentially ascending or descending through the frequencies in order, so if the control channel is displaying as LCN 3 and it is the third-lowest frequency in the system's pool, you might try assuming that and seeing how it works when you program the rest accordingly. If frequencies have been added to a system since it was originally configured then any ordered sequence which may (or may not) have been there to start with was likely thrown out of whack.
Finally, you might try posting in the regional forum which covers the particular system. It is possible someone has already figured it out and it was never submitted to the database here.
Good luck,
Jim