I haven't delved too deeply into this yet, so someone may correct me if I'm wrong...
In order to support switching on a SRX chassis cluster, you need to be running Junos 11.1 or newer. I assume you are?
I believe, and this is the part I may be wrong about, that you don't use ae interfaces on a cluster, you use reth interfaces and put them into family ethernet-switching.
The spanning tree config should be pretty straightforward, set the reth ports as members of the domain and set your root priority on the switch you want to be root.
*Edit: This would probably be better in the SRX forum, since switching on an SRX is a little different than switching on an EX, especially when clusters are involved.