first off, your motor is too small for a 36" boat
2nd im surprized you didnt burn that up first cuz 3500kv x 12cell(14.4V) = 40320rpms(if it has 80% eff.)
3rd if you dont understand something or are clueless on how to set up a boat, just post before you spend a bunch of money on nothing.
4th I usually like to have my boats running around 30000-33000 rpms(with 80% eff. counted in) so get a KBXL or fiegao(10xl-14xl) and use the proper amount of cells to hit 30000-33000 rpms.
Heres the formula to find out what rpms (guestimate, never really dead on)
KV x .8 x (Volts per cell x cells) = rpms
Heres the one to find out how many cells to run on a certain KV
33000 / (KV x .08) = volts

Hope this helps, btw, post some pics. The submerged drive has to go also. Youll never see good performance with one