For trunked systems, you're always better off programming the fewest control channels for your situation. If you don't travel a lot and the site you monitor doesn't change channels, stick with the one single channel that works. It will make things a lot simpler and improve reliability. Also, if monitoring trunked systems only, leave the squelch all the way down so it is always open: It will improve the control channel decode quality (forces the ADC to provide a constant stream to the DSP).
For figuring out systems in the future, it can be useful to program all of the frequencies as conventional in a scanlist. You can then determine the control channel (and, if necessary, the LCN order).