The flow will be determined from the return pump, not how you set up the dividers (at least in your diagram). The flow would be the same even if both dividers were the same height. If you want different areas of different flow, then you'd have to "T" off the refugium and control the flow with a valve or some other way as stated earlier.
BTW, because of how your design is set up, you are going to get LOTS of micro bubbles going back to your main tank.
EDIT:
After thinking more about it, I think I misunderstood what you were asking. The total flow through the whole setup won't change, but the currents may change in the refugium part with the height difference. I'm not sure it is necessary though (and may just cause more bubbles). My dividers are all the same height and from watching the particles and bubbles flow, I still get good circulation throughout the system. At one point, I did have another divider in the middle of the refugium part coming down from the top and extending into the water a few inches to help direct the flow, but found it to be unnecessary and took it out. HTH
John
