Ah I see - so it was what I understood the first time around :)
For example, IAP 1 is on VLAN 10 and IAP 2 is on VLAN 20. The ports on the switch that you have physically connected the IAPs to are trunk ports. Say IAP 1 is connected to gige 1/0 and IAP 2 is connected to gige 2/0.
For example, from cisco documentation:
"By default, a trunk port sends traffic to and receives traffic from all VLANs. All VLAN IDs are allowed on each trunk. However, you can remove VLANs from this inclusive list to prevent traffic from the specified VLANs from passing over the trunk. You can add any specific VLANs later that you may want the trunk to carry traffic for back to the list."
For your setup, you can do something like the following (this is from memory, so please check proper documentation for the right commands):
interface gig1/0
switchport mode trunk
switchport trunk native VLAN 10
switch trunk allowed vlan all except 20
This will prevent the IAPs from "hearing" each other and they will become masters in their own network.
Let me know if this helps.
Shashi