[brucepick]

I'm convinced that for this project to actually serve your driving needs, the deep cycle battery needs enough capacity to handle a typical day's drive, probably that would be to work and back plus a few errands. Of if your usual weekend drives are longer, you might want it sized to handle those.

SO -
If your setup has that capability, you don't need to switch the alt on and off frequently. Only for the occasional longer trip, or one that has unusually heavy use of lights and/or other electrical accessories. With that as a basis, I see it as not a big deal to pop the hood to switch the alt's output on/off, and to attach or detach the 4-pin connector. On occasion, not very often.

My alternator is unplugged and disconnected from the car's system nearly always. I find myself connecting it less than once a week on average.

Remember, if your deep cycle gets discharged so far that it needs to be charged before you get back home, you'll be charging it using gasoline - and that's exactly what you're trying to avoid with this mod. My system still has the regular starting battery, hooked up ONLY to the starter. It doesn't get very depleted from a few days use in starting the engine. If the deep cycle gets depleted, I can switch things over pretty easily without tools, to run the car off the alt and the regular starting battery till I get home.

That way the alt doesn't need to charge up a run-down deep cycle battery. Doing that regularly might wear out the alt; really it's designed to provide about 70-80A max current. That's to keep the accessories running as needed, and to top up a battery that has just started the engine, and then keep it topped up with a slight positive voltage charge on the system. Long term high current to charge up a depleted battery might not be ideal if done frequently.