Yes you can put in more than one site in the bank of a system. In fact, you can put in all the Control channel of the towers in the province. Like that, you never need to worry about what tower to program for your trip. There is a downside to this : by inserting all the CC, the scanner with stop on the first CC that is active andmight not be the one closest to you or the one you want to listen to.
That is how my Fleetnet system is set-up. I input all the CC of the province and I never need to worry about what tower to program Fleetnet when going on a trip.
Also, have a look at the feed I started on the subject : http://forums.radioreference.com/ontario/199589-provincewide-fleetnet-freq.html
There you can find the list of all the 32 CC that are use for fleetnet provincewide. Just program those in the system and you'll be good to go.