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Right now I have a 3000 Watt invertor wired to a 100ah sealed deep cell battery that I trickle charge at night.
My plan is to run #6 wire from the battery in the engine to the spare battery so the alternator can charge it too, but is this going to put too much strain on the alternator?
The most effective way to charge an additional battery from a single alternator is by use to a Split Charging setup.
You can buy kits from various sources and they are common amongst both campers, where a leisure battery is maintained and competition audio enthusiasts (ICE cars) whereby several heavy duty batteries to drive additional amplifiers make up part of the cars sound system.
Without a split charging diode in the circuit you have nothing to isolate your batteries and prevent strange behaviours as one battery approaches full charge.
I have three deep cycle type 31's under the hood and my 2000 watt pure sign wave inverter is on the transmission hump in the cab. Its about 15 feet from farthest battery to inverter. Based on the current my inverter draws 165 amps at full load, 300 peak. I ran 2/0 AWG copper wire with a marine multi chemistry regulator running the altenator. My truck starts right up with the 3 deep cycles, and depending on how many watts Im drawing on the inverter I can start the engine to add an extra 130 amps off the altenator. that will run a 13 amp 120 volt air compressor in case I need to fill tires or it can be used to power a skil saw if Im framing were there is no power. With a 3 foot copper stake driven into the ground that is connected with a 5' 4 AWG wire, I can generate house current and the outlets are GFI on the inverter. so I can work in the rain without doing anymore than poping a circuit. Or I can run a coffe pot or 700 watt microwave oven. Modified sign wave inverters will not run motors or computer equipment or medical devices, they also cost 1/5 of the pure sign wave. I can leave a 12 volt (all bulbs on the truck, including the headlights are LEDS) dome light on for 3 days or even forget to turn off the headlights for 3 hours before I would have a problem. So Ive never needed an isolater. They are all wired on one run, from the two batteries in the front left to the one on the front right and then through the fire wall over to the inverter. I have a quick release battery disconnect to isolate the starting battery if Im not going to park the truck for several days and that leaves two batteries if I need to use the inverter. I have never left anything on long enough to run all the batteries down. All the batteries are on one run, but the starting battery (Its a deep cycle) has the engine electrical connected to it, all three are on the same line. I had to use 32 feet of 2/0 AWG to make the 15 foot run.
A car alternator will be more than capable of charging two batteries. However you need to be more careful about connecting two batteries together if one is charged and the other is not. There will be no current limiting in the circuit, so you could easily exceed the manufacturers maximum charging current of the flat battery. Also to be careful of is if you did leave the spare battery connected while starting, it could be possible to try and draw a very large current from the spare battery which could burn out the wires to it if they are not capable of carrying the current.
There are two issues here. The first is if both batteries are low on charge then that would be too much for the alternator, but if only one is low then it would be fine. The second thing is linking the batteries will cause more problems. If you run the inverter from battery in the back then you run them from both. If you crank the engine from the front battery then you crank the engine from both. When you trickle charge the back battery then you trickle charge both.
There are some isolator options you can look into but a big fat relay can do the same job.
Couldn't you run 6AWG wire from the alternator through a 60 amp breaker, then to a 12v 30amp solar charger, then from the solar charger to the extra battery? This would isolate the back battery and not allow power to run to the front and also charge every time you started the engine. Both battery systems would be isolated but charge off a single alternator.
The normal standard way is to (USING A BATTERY ISOLATION SWITCH) that is a combo switch pattern that allows you to use either No1 or No2 battery! Then, a simple one easy operation you can use both/either of or even none if needed ... that way, ya got full & proper control of any situation you find yourself in [ I.e;- if any battery fails its duty or dies in its arse that needs replacing outya still have a full working system at ya finger/ hand tips readily to be used ] not matter wot happens in the system 👍 its the only way to go ! As with, ya got a seperate battery elsewhere, simply use an ‘ Anderson Plug, makes frucking around much more easier, to do .. ya problems are totally solved, if ya do it 😉 # and that's my way I have set up, without any headaches at al.
EDIT
Here is a example of what i am talking about, and for around $50 ya gotta ne bloody stupid, if you don’t get one... eliminates all ya headaches and buggering around to boot ! https://www.jaycar.com.au/4-position-battery-switch-with-enclosure/p/SF2248
