If you are referring to your new Uniden scanners and a Motorola system, it depends on wherther you will be listening from one location or many.
If you will be listening from one location, program the frequencies of the control channel you receive best. If you will be listening from several locations, program all the control channels of the sites you will be near. Then either way, set up groups of the talk groups you want to hear in the system. Define quick keys for the system and the talk group groups.
A third way would be to set up each site as its own system, but you might have to enter some talk groups into more than one system. Depending on how you want to monitor, this may be the best choice.
I put all the control channels into one system. If you don't like it, program the each site into its own system - but don't delete the first one. After using it for a while, you'll decide which you prefer and can delete what you don't like.
If you are referring to an EDACS system, you will have to define a system for each site to enter the LCNs properly.
I don't have the other models of scanners you listed.