To answer your question susinctly: No, you should not use flow-control between the two switches. It was not intended to be used for end-to-end flow-control.
HOWEVER: You may want to re-think your descision to use flow control at all.
HP Says: Flow Control was originally invented to prevent packet drops by switches that were running at less than media-speed.
Cisco Says: The problem Ethernet flow control is intended to solve is input buffer congestion on oversubscribed full duplex links which cannot handle wire-rate input.
Ethernet flow control is not intended to solve the problem of steady-state overloaded networks or links.
An example of where Ethernet flow control might be used appropriately is at the edge of a network where Gigabit Ethernet attached servers are operating at less than wirespeed, and the link only needs to be paused for a short time, typically measured in microseconds. The use of Pause frames to manage this situation may be appropriate under such circumstances.
Unfortunately, Ethernet flow control is commonly misunderstood. It is not intended to address lack of network capacity, or end-to-end network issues. Properly used, Ethernet flow control can be a useful tool to address short term overloads on a single link.
It will also "break" any QoS you may have set up for the hosts involved.
J.Cottingim