Wiring set-up for battery switch.
While waiting for the electrical experts to chime in, I''ll give you my simpleton view of things electrical. I think you''re making this too hard. Assuming you have a "normal" boat, meaning nothing with a huge engine that might require all kinds of amps to start,a deep cycle marine battery will do just fine to start the engine. What most folks do with your same (basic) set up, including me on my boat, is to rotate the use of the batteries. Battery 1 is the starting battery one day, and the house battery the next. Battery 2 is the opposite of course. The theory is you''ll always have a good battery to start the engine.
The main thing to do is to make sure you keep them both charged up as much as possible. Wet cell batteries like to stay charged, so invest in an onboard battery charger that will go to a trickle charge level when the batteries are topped off and won''t cook them by over-charging. Also invest in a digital meter so that you know the charge state of each battery.
Last thing -- don''t use that "All" or "Both" setting on the Perko switch as a matter of course while at anchor. Putting it on "All" and running your lights, the stereo, the water pump, etc. while at anchor will only lead to angst the next morning when you have two dead batteries that won''t turn over the engine. Always leave one charged battery to start the engine!
Oh...one more last thing: depending on where and how you want to sail/anchor out, etc., and how good you are at maintaining your batteries, you may want to invest in one of those emergency starter deals, like the Vector that''s in the West catalog (page 573.) For $60 you can always (well, as long as you keep this gizmo charged up!) start your engine even if your deep cycles are dead. I have one, which I mainly use to jump start my garden tractor when that battery goes dead. But I still have it for the boat if I need it.