Japanese 6-button layout, most players use index middle ring fingers for the top three, and then thumb middle ring for the bottom three.
On ye olde American 6 layout, a lot of players would use index for both the top and bottom left-column button, middle finger for the middle column of buttons, and ring finger for the two right-column buttons.
For any layout, certain fingers are usually substituted on other buttons during particularly tangled movements and awkward button combinations or sequences. This is where personal preferences are most likely to shine through.
Don’t be afraid to experiment! Just feel it out for yourself. You’ll be able to tell pretty quickly if any particular methods or techniques aren’t working out. Pay attention between hand positions that transition too slowly, fast movements that don’t give you enough precision, and positions that put a prolonged or exaggerated strain on your hand.
Things become messier for unusual commands that involve comparatively exotic inputs, like holding down buttons, timing button releases, double-tapping, pianoing, etc. Your hand will feel like it’s playing Twister with itself at a very lonely party until you get used to them individually, on a case-by-case basis. (Practice!)
It’s important to remember that you will see lots and lots of seasoned players doing lots and lots of different things with their fingers and hands. You can always pull ideas from them but don’t get caught thinking that there is one “right” way.
One of our city’s very best Hyper Fighting players does all of his button presses using all four of his fingers bunched together into the shape of a large pointy slapping mitten. I wouldn’t recommend his style to anybody, but he makes it work for himself! It’s pretty awesome. I hate losing to that guy. Hahaha.