Battery configurations are as disparate as which oil to run, but I have to disagree with running batteries in parallel when there are only two. Both batts supply more power in parallel, true, but more importantly they discharge together. If the alternator craps out with paralleled batts, the first indication you have may be when your electronics start shutting down or your motor won't start ... and by then you may be SOL. A boat spent the night off Charleston last year when this exact scenario occurred. By the time time they discovered the problem, the VHF wouldn't even work.
With a motor that doesn't exactly have a gorilla alternator (like Mariner, I believe), I'd run one battery as primary and one as an isolated reserve. Switch batteries as you will to equalize use, but BOTH (paralleled) should be reserved for emergencies only. BTW, modern switches are "make before break", and can be switched between batteries at will. DO NOT, however, SWITCH TO "OFF". You're always safe to switch with the motor off, of course. Perko and/or Blue Seas web sites should have wiring diagrams.
Starting batteries are fine if you don't have much of a drain, dual purpose might be a little better for your application, and nothing wrong with using two deep cycles. Starting batts don't do deep discharges very well, deep cycles don't like heavy loads but will tolerate typical starting loads OK. The keys to longevity is keep 'em charged properly, keep connections clean/tight, and keep 'em serviced. Lengthy application of chargers that don't disconnect at full charge have cooked more batteries than anything