"but sometimes I pick up other PLs not listed on RR. "
Maybe the ones not listed haven't been confirmed, also, they may not have been submitted by members yet
"Would it make any sense to program the same Freq on three different channels and leaving them in the CT search mode? "
I would program one channel as search CT(PL), one as seach DC(DPL). Use delay on those two channels, I don't think I'd set up three for PL search.
"Would it make any sense to program the same Freq on multiple channels and save CT codes everytime they pop up and label them appropriately as PD or FD or EMS, etc.? "
Thats one way to do it. Once you confirm a PL and its one you want to hear on a regular basis, program it and label it.
Lock out the PL and DPL search channels you've set up except for when you have time to sit and watch the scanner.
I have two different fire departments in my county using the same frequency w/different PL for each. I do have each one in its own channel. Other fire departments in the state use this same frequency some with PL, some not, so I have another channel programmed with the frequency with no PL, I have it locked out, because it would be too busy and block out the stuff I want to hear locally. However, I could unlock it if I travelled to those areas.