To answer the direct question, you can charge the two 6V batteries in series with a 12V charger safely. After all, the 6V batteries are just three 2V cells in series packaged in a single box.
If you go to redo the wiring, it is good practice to have a fuse as close as possible to the positive terminal of the batteries. This is to protect the wiring in case of a fault: the fuse blows before the wiring smokes. Blue Sea makes a fuse that connects directly to the battery terminal, you can't do better than that - but the holder and fuses are expensive (about $18 for the holder and $12 for the fuse). More common fuse holders can be mounted within 6" of the terminal.