In the .jad file that gets passed into rapc as an argument, there is a flag you can set to do this:

"RIM-MIDlet-Flags-1:"

The value you give the flag determines its startup behaviour. Right now, for example, I have an application that auto-starts up and is a system module. The value for that is 35. So in my .jad file I have the following line:

"RIM-MIDlet-Flags-1: 35"

The value is different depending on the startup hierarchy position you want your app to be in (1 - 7) and whether you want a system module or not. Experiment a bit and the above should make a bit more sense

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Aman