Don't use a switch, just run both batteries to two sets of large connections on the side
of your flight box to accommodate the large clips on the big starters but shielded so they
don't short. If you already have banana connections just use those.
Join them with the red jumpers for 12 volt use.
Use the green jumper for 24 volts.
Most 3 phase electric motors have a similar system for star or delta connection.
The current drain in the 24 volt mode won't be even but you could run the power
panel off one battery & the pump off the other.
Excuse the drawing (wife's laptop with crappy drawing program).
John.
Liam, the two 12 volt batteries will charge ok when wired in parallel from your existing charger
provided both are of similar age/condition, they will however take twice as long to charge.