I have a main battery connected to the positive terminal to an isolator to the positive terminal of a battery in the rear. Half the diagrams on the internet complete the circuit and connect the negative terminals, the other half seem to only connect the negative terminals to the ground. Is there a difference? If I add a third battery to increase capacity should I connect just the positives or connect the negatives in parallel as well?
The common is only via the chassis unless it is for very high amps.
An exception is if the battery is in the trailer then you have to connect two leads + and - to the car. The minus from the chassis or battery of the trailer to the chassis of the car or the negative of the battery.
Be sure you have a good connection at every point for both plus and minus.
If I add a third battery to increase capacity should I connect just the positives or connect the negatives in parallel as well?
In general, "just connecting batteries in parallel" by joining the positive and negative terminals is a very bad design. Unless the batteries are perfectly matched (which is never the case for real batteries) the voltage differences cause by their different charge levels, or even different temperatures, will cause one battery to do all the work, and quite likely also discharge itself charging up the other one.
This is not very effective for "increasing capacity," and if a fault develops (e.g. one battery starts to fail) the voltage differences can create serious hazards, both from high currents causing overheating, and the "failing" battery continuously producing explosive gases as the rest of the circuit tries to recharge it.
Common connections to one terminal are OK provided the wiring is adequate for the currents involved, but the other terminals need to be connected to a properly designed circuit including isolators (as with the OP's first two batteries).