Combining 12v Marine batteries of unequal capacities
Assuming that you are directly connecting the batteries in parallel, and the cables you use are adequate, the two batteries will always have pretty much the same voltage, and if they're the same chemistry they will discharge to the same level, and basically the whole combined capacity will be usable. If you take 50% of the combined capacity, each battery will end up at approximately a 50% state-of-charge.

Yes, the first approximation is that if the batteries have the same voltage, then they will provide equal current to the load, and that will cause the smaller battery to discharge more quickly. But, a battery's voltage lowers as it discharges, and any miniscule difference in voltage between the two batteries will cause a current to flow from the higher-voltage battery to the lower-voltage battery, through a very small resistance.

When you add the current from these two effects, what you see in the steady-state is that each battery will provide current to the load proportional to its capacity, because they're all trying to have the same voltage droop, and that any imbalance between the batteries will only be short-lived.

Here is an article from a battery manufacturer on "parallel operation of lead-acid batteries". (Actually series-parallel, but there's nothing to prevent a "string" of one battery). They state


  However, there is no technical reason that the individual parallel strings must all be of the same capacity. When battery strings of unequal capacity are connected in parallel each string will deliver power and accept recharge current proportional to its percentage of the total combined capacity as shown in Figure 3.


Their only recommendation is that each string (each battery, in your case) has an individual circuit breaker / fuse to protect against overcurrent conditions.

There is also a question on this SE from 2011 about charging lead-acid batteries in parallel, although it pertains to SLAs, and not marine wet cells.