If the 246 behaves the same as the 396, it locks on a given control channel (within one system) until either it is power-cycled or until the CC freq is completely unreadable - only then does it look thru the frequency list for other CCs. I have my radio set up similarly here in Calgary for our six-site Smartzone system. Even if I am directly underneath a tower booming out a strong CC, if my scanner was powered up in range of a more distant CC and it can still "hear" that one, it sticks with the original CC until I power it off and then on again.
I don't know if the game plan changes with you monitoring a VHF trunk vs. the 800 system I listen to. It might be worth your while to put whatever CCs you want into your one system for Fleetnet, and maybe - and I don't know if this will work, or is possible - set the attenuator "on" for the distant CCs, so they are less likely to be picked up when you're closer to another tower.