As far as programming... there are two ways that seem to be popular.
If you're going to be largely stationary, or if you want to monitor one site specifically more than the rest, then you may want to program each site as its own TSYS. This requires a little bit of effort when it comes to TGRPs, as you'll need to program them for each TSYS.
A more mobile-friendly setup would be to program the control channels for all of the sites you want to monitor into one TSYS. You'll then be able to use the multi-site features to determine when the scanner should give up on one control channel and search for a better one. You'll need to experiment with those settings... you'll want to use the "Analyze" feature to see how well the scanner is able to decode the control channel(s) so you can set the Roam thresholds accordingly to make sure that the scanner isn't constantly searching for a control channel.