I have been going through the same problems with my boat. I wanted to separate the curcuits and only run the starter from the starting battery and tie in the house curcuits a deep cycle battery. (I am assuming that most of you want a deep cycle as your secondary) But that has become very problematic. Not that it can't be done but I wouldn't have anytime to use the boat (Jeep, Truck) if I decided to rewire the entire thing.
Now correct me if I am wrong but therein lies the problem. If you want to run your accessories from a deep cycle batt without having to rewire EVERYTHING, you would have to have your deep cycle battery as your primary and have the starting battery as your back up. This would essentially connect the batteries when the solenoid is engaged.
I know very little about batteries and how they are made etc... However, my understanding is that one should not really mix battery types, sizes and so forth. Does anyone who knows more than me have any knowledge on the best way to hook this up? Is there a difference which battery is the primary when they are connected? Is there an issue with discharging your secondary battery "into" the primary when they are connected prior to starting the engine?
When the batteries are connected, will this act just like a dual purpose made battery? (Good starting amps and good amp hours)
I do have my own uneducated theories on these questions which are, likely deep cycle as primary is the most ideal way to hook them up. Charged battery will discharge into the drained battery but hopefully not fast enough at 13.2V to cause a problem so long as you are starting the engine right away. And yes they will act just like a dual purpose battery when connected.
This is how I plan on hooking them up in my boat and unless I am educated differently, then I will be a guinea pig of sorts.
Also a battery selector switch can be used which negates my entire post but leaves it up to the individual to manually switch batteries prior to starting and when the engine is turned off. For me that is a very easy thing to forget about.
Good timing on that question...my brother and I had this exact conversation this last weekend - he is installing a 2nd battery in his boat and wanted advice on the best hookup...
Everyone has a different opinion on your questions, here's my take...
Having 2 different battery types is bad when they are connected in parallel (either regularly or isolated w/the isolator engaged) without any charge current. The same can be said for 2 of the same type of batteries that are different sizes or ages - the key here is "2 batteries run in parallel, where one battery is stronger than the other, is bad - because the stronger battery will try and charge the weaker battery" - this is true even if you have two batteries the same size & age (like in my setup) and one battery is discharged more than the other. The stronger battery will always flow current to the weaker battery...
Now, let's talk about when they are hooked up to a charge source (alternator, charger, etc)...in that particular case, the difference between the two batteries is likely (likely, not absolutely) overcome by the charging circuit. Which means, if you have a house battery and a starting battery, they are ok to hook up together
as long as they are isolated when the car/boat is turned off. Hypothetically, if you were using a low-current charger and ran them together (with the isolator engaged), the stronger battery might be affected by the weaker battery, but that would only happen if there was a significant charge difference between the two batteries - so yeah, just use your boat/car alternator
Now, as for isolating switches...and I'll probably upset a lot of boaters here...but I do not like the manual switches (Off-1-2-Both) for any isolation circuit...for the exactly reason you said - 'Oops I forgot' can become 'How do I get back to shore' in a hurry...There are marine-grade automatic isolators out there, I'd suggest going with one of those...
If you want to be a guinea pig, go with the 500A isolator I listed earlier in the thread...I've been running that for awhile now with no issues...and I have my 2nd 80A isolator for my trailer run under my rear bumper (fully exposed to the elements) and haven't see it fail yet either...so you could hypothetically go with a car-grade isolator and hope it won't fail on you (your mileage may vary, and if you do go with one, check it regularly to make sure it's still isolating - generally when isolators fail, they fail in the 'connected' position, linking both batteries together).
As for starting/deep cycle - if your cables are big enough (ie 4 or 2ga), when you hook up both in connected status to 'start' your boat, hypothetically, your starting battery, even though it is hooked up through the isolator, should be able to 'feed' more current (due to the nature of the way it's built, that's why it's a starting battery)...you will still use some of the deep cycle to start the boat, but most of the energy required will come from the starter battery...note: use good cables!! If you use a crappy cable to the 2nd (starter) battery, the cables will act as a restrictor and your 1st (deep cycle) battery will be used more...I hope that made sense
My brother decided to go with a manual switch, located right where he can see it every time. He's going with starting battery to start the boat, and deep cycle for his boat circuits (he has them run separately already)...personally, I don't think the type of battery matters when they are wired correctly, and I already told him not to call me when he forgets to turn the switch and wears down both batteries listening to the radio and running his fridge all day on the 'both' setting