You can include a line, in the config file for your ISS (found in the "[MainOrbiterDirectoryName]\config\Vessels" subdirectory):
Maxfuel = x
(where "x" = number of kilograms of propellant, to be carried by ISS)
Your ISS will then always have that much fuel (available to be transferred to your ship, using FuelMFD) at the start of any scenario, as long as the scenario file includes, under the entry for the ISS:
PRPLEVEL 0:1.000
("1.000" means that the scenario will begin with ISS carrying 100% of Maxfuel. You can decrease the amount, with which to start the scenario, if you want. The amount carried, will be depleted as you transfer the fuel to your ship.)
I have my ISS (ProjectAlpha_ISS, actually) config'ed to carry Maxfuel = 50000, which is a bit unrealistic, I suppose, but it is then always available as a refueling station.
The same thing can be done with Mir, and perhaps other space stations.