I think the HomePatrol-2 (and definitely the SDS100) should have the sites programmed separately. Uniden scanners are usually set up to cycle through all the sites that it can receive, so you will be able to monitor both sides of the system without much issue.
The suggestion to program separate systems mostly applies to scanners that find one site and just park on it without checking other sites, which are pretty much the Whistler TRX and related GRE models. It also applies to older GRE/RadioShack models which might not be taking advantage of the stationary multisite mode.
Programming all of the control channels into a single site on a Uniden scanner will lead to weird behavior that would copy the Whistler behavior of only being able to lock onto one site at a time. The reason for this is a single site can only have one control channel at a time, so the scanner will find the first good control channel for the "combined site" and then skip checking the rest of the control channels to save scan cycles because it is not possible for one site to have more than one control channel. This would cause the exact issue of only being able to hear one side of the system at a time that we are trying to avoid.
This behavior for the SDS100 has been tested in the thread
SDS100: - Curious about what would happen.