what to do with weak flush oop?

[awakuni]

i badly misplayed a hand at commerce and wanted some help as to figure out what to do with a weak made hand next time. i had 3 9 of clubs in bb. there were five limpers, so i checked my option (there's now $10 in the pot). flop comes ace high with one club and one three and its checked around. turn comes king of clubs. mp position bets $5 and everybody calls including me ($35 in pot now). river comes jack of clubs and sb fires out $5. here's where i feel the confusion, because i have a nine high flush and i don't know where i am in the hand. i think i'm ahead but because i'm not sure i just call. i'm also thinking that i may want overcalls. i don't know. if somebody could help walk me through the hand i would be super grateful because i feel like i really messed up a good money making opportunity.