Heya Thorn
I've purchased & installed several cheetah alarms off an ebay guy in singapore and installed them on a few bikes, including my TBA. I did so by using the bike's built in alarm wiring (I cut off the connector and soldered directly since that connector's impossible to find aftermarket). The standard wiring allows the alarm to imobilise the bike by breaking the connections to both the ignitor and the starter motor. Because the cheetah alarms only have one imobiliser circuit I chose to use the ignitor circuit which means you can still sit there and wind the bike over with the alarm screeching but it'll never run.
As soon as you use an alarm with remote start you completely change the way the alarm's wired. Typically these alarms need to have the ignition switch & start button overridden by the alarm to allow remote start, and to have the live wire to the ignition switch cut and redirected through the alarm module to allow remote shutoff. If you've not cut & rerouted that wire through the alarm you'll have remote start, but it can't shut down the bike.
As for sitting the bike upright, I'm not familiar with this alarm but many only have a shock sensor to put it into alarm mode if the bike's hit. Detecting the bike gently being stood up required a tilt mechanism, which of course won't work if you put a bike on its centre stand (for those that have them). Does the alarm have a seperate wire to secure accesories like hard bags? If so you can purchase a mercury tilt switch from any decent electronics shop, connect that wire to the switch, and connect the other side to the bike's earth to act as a tilt detector.
I have a write-up describing how I fitted my alarm to my TBA, including a table showing the connector description
here. Hope that helps you some. If you still need help you can post the alarm's instruction here (or email it to me privatley) and tell me how you've connected it and I'll see what I can do to help.