Ideally with a 2-battery system you have one battery for "start" and one battery for "accessory", managed by a dual battery "black box". When set up this way, your start battery will never fall below a certain voltage and always be available to start the vehicle, while the the accessory battery will be allowed to run down to the minimal voltage level (around 10VDC) to keep powering offroad lights, radios, etc as long as possible. An engine start condition could also employ both batteries in parallel, either manually or automatically, depending on the battery management "Black Box" you choose.
Because such a setup is specifically designed to handle batteries of different charge levels, there won't be any issues with battery life.
When you have a simply wired system with two batteries in parallel (2x 12V parallel = 12V total at twice the current) it's critical that they both have identical states of charge. If one battery is lower charge than the other, it will drain the other battery. If one battery has a bad cell it will permanently cause the other battery to drain down regardless of the charge rate or health of the alternator / voltage regulator. So, you should always replace both batteries at the same time and be careful that one does not have a failure of some type (sulfation, for example).
The 2 in parallel system can work, but it is not as reliable as the system with a battery management box, where you would instead be free to replace just one battery or to use two batteries of different health.
Care should be taken so that the wiring can accommodate the higher current capacity. For example, if the wiring to the starter solenoid and starter itself is only sized for a single battery, you will not be able to avail yourself of the starting power of the two batteries completely, plus it is a fire hazard. If the dual battery setup was OEM it is probably OK, but if you are retrofitting a system yourself, a wiring upgrade is in order. OEMs do not normally build in extra capacity when it comes to wire size, because for one thing, copper is expensive and OEMs are cheap, and for another, copper is heavy and OEMs are all about minimal weight. You might think a little wiring is no big deal, but the modern vehicle has miles of wire, and it truly adds up.
Note that if you are replacing wire, the correct SAE grade wire has the proper insulation for automotive use. If you choose instead to use AWG grade wiring, know that AWG 20 (for example) is heavier and larger in cross section area than SAE 20, but it may not have the proper insulation suitable for automotive use. Avoid trailer wire (which is often the only kind an automotive store sells), which is not rated for under-hood or automotive interior use.