As has been alluded to, when you have batteries of differing states of charge and/or capacities, the electrical energy in them will always try to be equal. In other words, if you have an older battery and you connect a newer battery to it, the older battery will feed off the new battery for its charge. As batteries age their capacities diminish. So, when you place a load on the batteries, the old battery will be drawn down faster than the new one (Peukert Effect) and will feed off the new one, making the new one work to both sustain the amp draw on the bank, as well as to feed the older battery at the same time. The end result is, the lifespan of the newer battery is dramatically reduced, and the end-of-time for the old battery is likewise dramatically accelerated. You're burning the candle at both ends.
Always replace batteries in a set, of the same manufacturer, type, capacity and date of manufacture - same lot if possible. Always start out with more batteries than you think you'll need, because you can't just add new batteries to old for the reasons outlined above. If you start out with 4 batteries and then 18 months or 2 years down the road you realize you need 6 batteries, you can't just add a couple of batteries. Instead, replace the older 4 batteries with 6 new ones.
As to the original poster (Vipra), make sure you have a true isolator and not a simple continuous duty solenoid. Second best option is a battery separator.
In the case of either a separator or an isolator, which combines the batteries into a single system so the alternator can charge them all at once, the charging requirements must be the same for the starter battery and the house battery.
For example, most starter batteries require constant amps (30 amps max, usually between 10-20) and variable voltage, while AGM deep cycle batteries require constant voltage and will handle variable amps. The voltage requirements of AGM's are vastly different from that of a cranking battery, so when you combine batteries via a battery separator or isolator, both batteries are gonna get the same charging voltage and amps. Ergo, both batteries had better have the same charging requirements.
So, with batteries combines and the key turned on and your running down the road and charging the batteries, whatever you're pulling from the house bank (fridge, whatever) is also pulling from the starter battery. Not to mention that the starter battery, which will recharge usually in a matter of minutes, will be subjected to the same charge (and hence, overcharge) as the house bank, whether it needs it or not. Also, when combined via the isolator or separator, even though both batteries are being charged by the alternator, the house bank is also pulling from the starting battery at the same time, putting further stresses on s starting battery.
The ideal solution is to use an external programmable voltage regulator (programmed for the charging requirements of the batteries you want to charge) and use the alternator and that regulator to connect directly to the house bank. Then, using something like a Xantrex Echo Charge or a Balmar Duo Charge (both of which are also programmable voltage regulators) you connect the house bank to the starter battery, thereby allowing each set of batteries to be fully charged and discharged independently.
Slow and steady, even in expediting, wins the race - Aesop