Find out what route your fleet is going to take and pre-position a "Supply Flotilla" at the last stop and re-fuel there before you go in, once you have the upper hand, bring in the Supply Flotilla to some planet/moon close by and by the time the combat is done the SF is there....both the Battle Fleet and Supply Flotilla were on manual control.
My Supply Flotilla consisted of 3 Tankers and 1 escort(very quiet sys.

One thing I should add, I had to manually grab one of the tankers and run around fueling the ships.
Would be nice if the Tankers had a command to "Fuel all ships/Fleet nearby". Maybe have the Fleet name as one of the options.