I've installed 3 different alarm systems made by 3 different companies and all 3 had a designated zone for smoke detectors which they recommended you use rather than separate them. There must be good reason for doing it this way. I would say that having your alarm know which part of your house was on fire would only be useful if your house was beyond rediculously huge. Like 50,000sf or more. Anything smaller and it would seem to me that the smell and sight of smoke/fire would likely tip you off far before you would even think to start scrolling through menu screens on your alarm panel.
In short, I would do it the way everyone else does it. It's just too important an alarm to find out there is a glitch because you did it different.