You can assign preferred tuners to each channel. Tucson channels should have different names and channel numbers from those Phoenix channels. So if you record a show specifically from a particular channel, you should not have any issues after you assigned a preferred tuner to each channel. If you choose to subscribe, and use "All channels", then there may be a problem. You can try selecting as many specific channels as you want, instead of choosing "All channels", but order the selected channels. MC picks a channel according to the order you picked when multiple channels air the same show at the same time.
Ordering channels during recording setup is a bit non-intuitive. You need to open the drop-down, pick you first choice, close the drop-down, and then open it again to pick your second choice, etc. - unless the channels are already ordered the way you want them, in which case you can pick them all at once.
