I had a hard time with this as well and here is how i aproached it... first thing you could try is using the geofencing capability, I've found its not very accurate/consistant though, but if you can get it working for you, great!
The current way i do mine is, I first looked at the "most likely" break in spots for my house. For me, its my back door. Luckily, this is not my usual daily entrance. Then I also look at the least likely break in spots. My garage door and my front door would be very difficult to break in to, so I use those as my disarming. If my deadbolt on my front door is unlocked, it turns off the security system. if someone kicks in my door, it will still be armed and the alarm will sound. If I open my garage door, it deactivates my system. if someone somehow smashes through my glass block windows and gets into the garage and opens the basement door, the alarm will sound.
now, what I'd LOVE to see built into this software is the capability to check the status of a device during the sequence of a scene. for example:
Door opened during armed status --> Alarm scene activated (delayed alarm) --> you enter house and push a button to deactivate armed status --> Alarm scene checks status of ARMED status after a delay, if false, alarm does not sound, if true, alarm sounds.