I agree with Bill Roosa - bigger is always better. This does assume space to install them properly.
If you double the size of a battery bank and waste power in one way or another they will take longer to charge. But for a given power usage the larger bank will be discharged less and last a lot longer. The cost of the extra battery or batteries will be more than offset by length of service they give you.
Bingo, bingo, bingo we have two winners!!!!
Your batteries are wired in parallel, not series. I am not sure what you mean by "..both have isolators..."
If it is a battery isolator with the alternator output wired to one lug with the 2 outputs going to each battery like pictured below definitely get rid of it. The best solution to effective charging is to use an ACR or Echo Charger between the banks and wire the alternator output directly to the house bank. This makes proper charging of all batteries automatic. Or alternatively use the 1/2/both switch manually to charge all batteries with the associated risks.
You do know that diode isolaters were invented by battery companies, to kill your batteries early, so they can sell more lead...

Maybe not but they might as well have been... Dumbest invention for marine batteries ever....
I am currently in the process of replacing 10 AGM batteries that were MURDERED by a diode isolator, undersized wiring and a Hitachi alternator.. The poor owner got just two years out of a $2800.00 set of batteries. The folks who did the install simply dropped the AGM's in-place of flooded...... It was amazing he even got two years but this was only because his shore charger did not pass through the isolator and they got to 100% a few times per year....
Seriously a larger bank will last longer and be a significantly more efficient bank to charge vs. the smaller bank. This of course is within reason. A good rule of thumb is to size your "loads" then add another battery or another 100+ Ah's.. This will take you to shallower average discharges.
No one ever talks about the Peukert effect, because most don't get it, but it is a HUGE benefit to a larger bank....
Some things to consider:
* No bank will ever get to 100% via alternator unless you motor for 10+ hours
* A smaller alternator on a larger bank will remain in BULK longer. This makes it run at its most efficient state for LONGER.
* Charging a smaller bank more often vs. a larger bank for a little longer there is NO COMPARISON which method is more efficient. The larger bank charged less often and for slightly longer is the MOST efficient. We can't forget 20-30% charge inefficiency so when charring more often you lose more.
* The larger bank will be discharged less so cycle life will be longer.
* The larger bank makes capacity gains from Peukert effect thus you gain capacity beyond just the face value Ah rating.
Simply put a larger bank with smaller average loads will survive better than a smaller bank with the same "average load"...
Take a parallel bank of 4 X 100Ah batteries. You now have a 20 hour rating that can support a 20A load, or 5A per battery, X 4 = 20A. When you run this bank at an average load of say 8A you'll really have 503Ah bank NOT a 400Ah bank..
If you add just one more battery and make the bank 500Ah's and you'll have a 25A support load (at the 20 hour rate), BUT, apply the same 8A load and you have a bank that can deliver
665 Ah's using an average of an 8A load.
Conversely, size your bank small at 100Ah, which would have a 5A support, and still apply the same 8A load and you really only have an 89 Ah bank. Bank size vs. load matters and the bigger bank results in a lower Peukert corrected load. This means less capacity is used with a larger bank and the shallower the discharge cycle will be. Shallow discharges are good for the battery bank and deep discharges are bad.
If you keep your same charging schedule your alternator will still be in bulk longer, which is more efficient, and you still need to replace the SAME capacity you took out..... Instead of hitting "limiting voltage" at 75-80% SOC the larger bank with the same charge source may not hit absorption/limiting voltage until the 90% SOC range due to the current / Ah capacity ratio......
* Batteries should match if put into one bank. Match battery brand, battery model and date code!
* No diode isolators!
* Bigger
is better, within reason!
* Charge them properly!
* Maintain them properly!
* Wire them properly!