I know that puzzle! :)
The separate pair of 6s will be fine except for charging them at the same time as the main bank. "Depends" on your set-up.
You can have longer links between one pair of batts than the other pair has between them. But now how do you attach the loads with three 12s? There is a proper way but not very convenient.
Bottom line is, wire them up however works best in your own set-up. "Perfect is the enemy of Good Enough"
BTW when linking a low set of batts (12.1v) to a fully charged set 12.7V) the "spread" is 0.6v, so you don't get many amps! Takes hours and days to equalize their voltages. Forget all that.
You can jumper the two batts onto the four batts whenever you happen to be charging the four. That will get something done. "Depends" if that is enough.
Story is you can do anything you like --it all works. Just takes time and a bit of effort.