For your WS-1040 & -1065, you can enter the control frequencies for more than one site, as long as you program it to check all the sites instead of stopping on the first active control channel it finds. Program your frequencies into the site, & set it as "Multi-site". If you tag that as "off", the scanner will check for a different control channel each time that system is scanned. Or, if you tag Multi-site as "On", the scanner will use each active control channel to check for activity each time that system is scanned.
For the 325P2, you enter each site separately.
Simulcast can be a problem in some cases. Neither the two Whistler scanners, nor the 325P2, handle simulcast well. But,
simulcast distortion is extremely location specific, so they may work if you 'win the simulcast lottery', and are in a location where it does not affect you.