You can install a pressure reducing valve with a downstream sensing line upstream of the skimmer to provide a constant high pressure to the skimmer.
Running a separate pump may prove more cost effective/convenient/reliable, but you absolutely can configure the system with one pump as long as it can provide high enough flow at a high head.
I don't know exactly what you mean by flow gauge for 500+ gallons, but if you mean 500 gallons per minute, there a ton of options out there.
A venturi nozzle and d/p cell or d/p gauge would be the simplest. You may be able to purchase one calibrated for seawater, but if you can't find one cheap enough, you can calibrate it yourself with a flow totalizer or by pumping a known volume at the same head as the system. Magnetic, turbine/paddlewheel, and ultrasonic systems are out there too. A portable ultrasonic unit could provide measurements at any point in the system.
Here is a link to a book which gives instructions on building a venturi flowmeter for aquaculture systems:
http://books.google.com/books?id=P4...qYvLIG&sa=X&oi=book_result&ct=result&resnum=2
www.omega.com sells units ready to install.
if you want metal one, cu-ni or monel would work fine.
if i were you i would just build all the tank discharges with the same outlet pipe size and make an orifice/pressure gage cap which you could use to ensure all the tanks had equal or sufficient discharge pressures.