at layer 2. HSRP will affect the layer 3 traffic. So once the wireless traffic is pushed through the trunk from the 4404 to the 6506, the vlan that it corresponds with will then be redirected via the primary hsrp partner for the subnet that the vlan (for the wlan) goes through.
We run a very similar setup, 6506-E hsrp pair, 4 4402 controllers. vlan/subnets are balanced between HSRP partners.
Switch A is primary for odd numbered subnets/vlans, Switch B is primary for even numbered subnets. We go as far as to number the vlans to correspond with the network octet - vlan 23 = 192.168.23.xx for example.
Are you Implementing VSS in your 6500 setup ? If yes, then it will behave a single chasis. The reason for asking is - 5508 when working in LAG mode puts all its 8 ports in a single port channel. you can not put the port coming from WLC to the 6500 in seperate switch if they are not in VSS.
So, first of all, pls update if you are running VSS or both the WLCs will be plugged into different chassis ?