Let me see if I can answer your questions and others I think you might have later on.
1. Banker's Hall is the main site, site #1. It is the one that will carry the most traffic.
2. No, Banker's and Forest Lawn are not only backup sites - they carry regular traffic as well. However...
3. Yes, the backup talkgroups are only heard on these sites. I'll explain that in a moment.
4. If you set your 396 to Control Channel Only mode and load only the CC's and alt CC's, your radio will work just fine.
Now ... to talk to some points.
The backup stuff: Each agency has a handful of channels that only work on certain sites (by design - the radios are programmed to use only that specific site when a user switches to that channel on his channel list). As I write this, I'm not 100% sure if a console user (dispatcher) originating a call might be able to transmit a backup talkgroup on all sites.. but anyway, the two backup sites are Banker's Hall and Forest Lawn. I'm not sure why Forest Lawn was picked - maybe because the lion's share of Calgary's residential population is concentrated in the NE - but the Banker's site is the primary backup because it is the tallest and most central site in the city. The idea behind having backup comms only on one site is so that if one (or more) of the towers gets isolated from the main system - a situation known as "site trunking", where a tower is still operating but not communicating its transmissions to the other towers/sites - then with the backup comms only on one site, you will not have to worry about other outages/problems screwing you up even further.
Another thing to remember for those who haven't monitored a Smartzone system before is that not every talkgroup is active on every site, for every transmission. To reduce the amount of frequencies and radio signals used, only towers which have radios affiliated to specific talkgroups will hear/transmit that talkgroup's comms. The exception is as mentioned Banker's Hall, and as well, some talkgroups can be (and have been) programmed to transmit on all sites all the time. Anyway.. for example, if I am on C16 in my fire truck in Redwood Meadows, hitting the TransAlta tower on Broadcast Hill, and talking to 71 Pump who is in Springbank, hitting the Spy Hill tower, and nobody in the south half of the city has C16 turned on on their radio, the Fish Creek tower will not broadcast C16. Now, if 26 Pump suddenly pulls out a portable and tunes it to C16, then you will hear those comms on the Fish Creek tower as well. There has to be a radio tuned in to that talkgroup in order for a site to receive it. Like I said, it's especially useful for limiting the amount of resources (frequencies and airtime) used - the less the Fish Creek tower is transmitting, for example, the Airport Authority parking garage channel, the more resources are available on FC for other talkgroups. What does that mean to a scanner user? If you know something is going on on the other side of the city and you can't hear anything on that channel, try switching to another tower site closer to the incident (if you can). If you can't, you may be SOL, unless someone with a 'real' radio tunes in in your zone.
If you choose to put all six sites into one system on your 396, be aware that it will not automatically switch to the strongest site every time the scanner hits that system. Once the 396 is turned on and captures a good CC for a system, it will always go back to that CC unless it completely loses the signal for a certain amount of time, or is turned off and then on again. So if you start out downtown and lock on to Banker's Hall, then move south into Fish Creek's territory, your scanner will still weakly get BH's signal - and your reception will be crap. What I do in that case is turn the radio off, try and shield it from receiving Banker's somehow (usually standing between the antenna and the tower is a good way), and turn the radio back on. Then it should capture FC properly and your signal will be decent again.
Why would you bother putting all six sites in one system, you ask? Mainly so you don't have to fart around with six sets of talkgroups. I tried that (putting each tower in as a separate site) for about 2 days when I first got my 396 and it drove me up the wall - if I wanted to switch Police on, or lock out a CFD tactical talkgroup, or whatever, I had to do it six times in a row! Think about doing it on some of those ridiculously huge systems like Ontario's FleetNet or the Nevada Shared Radio System.
Last but not least - if you have not done the firmware upgrade from this past spring for your 396, I strongly urge you to do it if you intend to listen to Calgary DRS. The P25 (digital) audio on 753f is much, MUCH improved after the firmware upgrade than with the v1 396.