If you're using a diode isolator, your voltage regulator is always connected to the starting battery bypassing the isolator (this is necessary due to the voltage drop across the diode). Hence, as long as your batteries aren't drained enough, and your load isn't heavy enough, to overpower the alternator's capacity, it's going to put out a steady 14.5V or so (depending on your regulator setting), and the flow through each leg of the isolator will be proportional to that branch's ability to accept it.

In other words, if your starting battery is discharged enough to accept 5A at 14.5V, and your running load on that side is 20A, you're going to get 25A on that diode. If your house bank is drained enough to accept 40A at 14.5V, that's the current you're going to get through the house diode.

If you're wondering how that side "knows" to get 40A, you're actually overthinking it a bit. Essentially, the current is going to keep going up until the voltage necessary to put that much current into the battery is the same as the fixed voltage coming out of the alternator.

If your house batteries are so heavily discharged that you are well above your alternator's capacity, all of your alternator current will end up going to your house batteries, while your running loads (engine ignition, headlights, etc) will temporarily run off of your starting battery. However, your house battery will not directly drain your running battery. Once the charging voltage on your house battery comes up to equal the voltage your start battery is putting out while temporarily running your engine, the starting battery side will start getting a share of the alternator current as well.

To make a really silly joke, your charging system with a diode isolator system is very socialist; "From each (alternator) according to his ability, to each (battery) according to his needs."