What do you mean?  Are you asking, "How do I increase my fleet supply?" or are you asking "How do I increase the maximum fleet supply above the number you would get with the Large fleet supply setting?"

If you're brand new to the game and wondering how to increase your fleet supply, the answer is to find the Fleet technology tree where you will see two progressions of 8 research steps each.  The one on the bottom is for your fleet supply; the first increases are cheap.  Do note that when you increase your fleet supply you increase the amount of credits, metal, and crystal lost to taxes.

I'm pretty sure you can make some simple modifications in one of the game's setup files but I don't know which ones or what.  You should post your request on the Modding forum and I'm sure you'll get lots of helpful responses.  (There's probably even a mod or two out there for it.)