1. Managing the switches should not be a problem if all the switches have their sc0 configured to be in the same ip subnet as that of the management workstation.
2. I am not too sure I understand when you say `all switches and routers are in one ip class'? Do you mean to say that all your routers connect to your other branches with dedicated private lines (like frame relay etc)? and hence all the ethernet ports have been kept in the same class of subnet?
3. Anyway you should not have any problem of routing as long as your 6509 is doing its job of Layer3 functionality.