Whilst I am no expert, my experience with Link 20 is that it has two shunts that measure current flow. The way they need to be connected is with the negative cable from each bank running to one side of each shunt and the other side of the shunt connecting to the ground bus.
ALL negative feeds from ALL circuits go to the ground bus of the battery they are fed from and NONE to the negative side of the batteries. Then there are a number of other connections that go to the positive sides of the banks, I can't remember them all but the installation instructions are reasaonably clear. If you want I can PM you the said manual.
What is important about the first paragraph is that any device that leads back to the battery negative will not be "seen" by the Link20. So in short, only one cable must be connected to the neg side of the banks, that is the fat battery cable that runs to the Link shunt.
My 1-all-2 switch only controls the charge to the banks and the postive feeds to the appliances. The Link does not differentiate where this switch is set. You can pretty much set this switch up as you choose. Mine is set up with the whole house bank on 1 and the other bank on 2 but you can split your house bank into two if you can find a valid reason to want to
Also, Link20 allows you to set the size of your banks in terms of amp hours and the Link will better be able to calculate the remaining capacity. You can also reset the amp hours to zero any time you choose and start the consumption calcs from base. These settings are also clearly descrbed in the manual.
Hope this is of some value although your description above does sound a little like a can of worms.