Dear Dazed,
The only way to figure it out is to trace each wire to its source. The 3 big red wires on the back of the control switch should go to 1) battery #1, 2) battery #2 and 3) to the DC panel. The terminals are marked on the back and it matters that the terminal marked "common", "both", (1+2) or the terminal NOT marked with #1 or #2 goes to the DC panel. The terminals marked 1 and 2 go to batteries designated as 1 and 2 by you, does not matter which is which. The switch will select battery #1, Battery #2 or BOTH to supply power to the DC panel. You mentioned three batteries and "series". You should have two batteeries in Parallel on position 1 or 2 and a single battery on the other position. The switch connects battery positions 1 and 2 in Parallel when on BOTH. Parallel doubles the capacity, series doubles the voltage which is bad if the batteries are already typical 12 volts. If you really do have 2 batteries in series at one of the battery positions and they are not 6v golf cart batteries, you are putting 24v dc into the system with the 3 way switch on that battery position and on BOTH.
If the above is the setup, the issue(s) is with the connections from all the lights, etc to the dc panel (normally where they connect) or to wherever they actually connect to get their 12v dc, like the engine panel or maybe direct to a battery - not normal for most circuits.
The big, but very useful job is now to trace each wire from the load back to it's source of power. It should be a breaker in the dc panel but could be anywhere. Check for marginal, corroded connections. Bad breakers. Check that each circuit at the DC panel is firmly connected to the bus bar or breaker. Trace the ground wires and check their connections for each load as well. They probably connect to a common ground at the dc panel. Make sketch or diagram for reference later. You will soon understand where it all runs and why it works or doesn't. You can label it all as you go if you are ambitious. Once you've done this once for each circuit you probably won't have to do it again unless you find something you need to correct which you probably will.
It shouldn't be too big a job on an E27. As Loren suggests, a complete re-do is something to consider if the existing wiring is a total wreck and/or you just need a bunch more circuits.
Good Luck and let us know what you find.
Mark