If you are starting on the deep cycle alone, compare the CCA of the deep cycle battery you select to the requirements in the Yamaha owners manual, battery rating should be equal or higher.
With few exceptions, there is no reason to use the BOTH switch position when starting.
If you have a reason to run down your starting batt on house loads, it will not recover fully.
G02Marine.com has a special - delivered to the door deal from distributors for Interstate batts. Just got their email.
I have two of the flooded marine series 29 deep cycles, rated to crank also my HPDIs just fine.