First, just an explanation of why opposite end connected loads will help balance the battery bank:
This diagram illustrates the advantages to this wiring arrangement. So long as each pair of conductors from battery to battery is equal, the load sees the same resistance between it and each battery. Just start at either load connection point and follow the shortest path through any battery. Disregarding the internal resistance which is only shown to illustrate the connection, you will have 15 ohms, even if the distance between the batteries varies.
In addition to this precaution, if your batteries are lead acid and of a type you can easily maintain, perform maintenance on the old ones when you add the new one(check and top up the cells) and if you don't already have one, arrange a schedule of routine maintenance.
If they are sealed or non lead acid, consider replacing the original two when you add the third. Lead acid and NiCad are probably most tolerant to skipping this, but if using aged batteries with new ones, at the very least you should monitor them regularly.
Now, if the batteries and load connection are in any other arrangement, such as having the load connected to the same battery, any other battery in the bank will certainly have more resistance between itself and the load. This resistance will prevent that battery from discharging as quickly, So the closer battery to the load will go into a deeper state of discharge before a given voltage is reached, causing greater wear, etc. The more resistance and volt drop difference, the more aggravated this will be. To minimize the effect you might have to keep the volt drop orders of magnitude lower by using much larger wire so that instead of being balanced, volt drop is negligible.
The remaining flaw with the end connected arrangement is that if each battery is providing equal current, the interconnection wire closes to the load connection point carries 2/3 of the load current, and the wire farther away carries only 1/3 load current. If the difference in conductor length was as great as in the diagram, a 2:1 ratio, there will still be some difference in the voltage drops between each battery and the load. Your Setup B, though it has longer total length and may require larger wire for that reason, is likely the best possible arrangement because it promotes balance in the lengths of the conductors between batteries.
Now all that remains is to figure out what size wire you need. Figure out what the resistance of the original wires was using a wire size chart that has resistance in ohms per unit length or calculate based on cross sectional area. Now figure out what length your wires must be to connect all 3 batteries as in setup B while keeping the length of all 4 of them as similar as possible. Then calculate how much resistance per unit length can be tolerated by dividing the old total resistance by the new length. Then return to the wire chart and check what size wire you need. Note that two of the wires carry twice the current of the other two, so there will be some difference in voltage drop, but the current through each battery must pass through one wire of each type so they stay balanced.
While you're at it you could check your maximum total load current and figure out how much volt drop you have over these cables and base your decision on what size wire to get partly on that. Square the current on each wire and multiply by the resistance to see how much wattage is being used, and divide that by the total load wattage. If it's more than 1% or so of the total you might want to increase the wire size further. You generally only buy the wire once, but the batteries cost a lot too and while you'll have to replace any battery eventually, treating them well could offset a lot of wire cost.
