I'm thinking two buttons in the market interface; "Resupply" and a gear icon. The gear icon adjusts your fleet's "default" levels for supplies, fuel, and crew. Clicking "Resupply" will buy first from the Military then Open markets to raise the player fleet's stock to the defined levels. Perhaps it should "queue up" the order the same as normal market interaction.
I'm one of those weirdoes that when I have less than x supplies, I want to buy exactly enough supplies to have x. The best way I've found to do this currently is to queue up selling my stack then shift-dragging x supplies back to my cargo, then again for fuel and crew.