Hi Neil
1- Are you using Cisco Server Load Balancing (SLB) by let the Cisco 6506 assing Virtual IP for a Virtual Server combines of all your Server Farm.
In this Case, Check SLB configuration on the Both of the Cisco 6506.
2- Or you are just connecting Each NIC in the server to the cisco switches.
In this case are you using Trunking configuration for Higher speed (Then check Trunk configuration between Cisco 6506 and Servers).
And if you are not using Trunking, then you are connecting each NIC to the 6506, so you have multiple Subnets and you have additional work involved because most machines will have to be reconfigured to take into account the split, and to know that traffic destined for the other subnet must now be routed through the router instead of being sent directly.
More explaination or if possible a network diagram will be helpfull my dear.
Good Luck!!!