Tugboat Serenity
I guess you have a speed controller!
You need a fuse rated to blow before the speed controller does.
Your fuse ( if you fit one) needs to go in the positive lead to the speed controller between the point where the two batteries are joined and your speed controller.
As to its rating have a look at the Amperage your speed controller is rated at and fit the nearest value you can find to that figure.
"that's not a bug its just an undocumented creature."
Sir Terence David John "Terry" Pratchett, OBE (28 April 1948 - 12 March 2015)