The new deck mount goes on the battery bank and the existing wires from the battery bank to the DC fuse panel stay as is. You can leave the "lower portion" converter part of the WFCO in place and just not use it.
The DC-DC output also goes on the battery bank, as does any solar controller's output.
You might need a positive buss bar to hold all the wires and just one fat wire from that to the battery. All the neg wires go to the shunt for your battery monitor including the wire that goes from the frame to the neg battery post now--it will go to the shunt and only one fat wire then goes from the shunt to the battery neg. If the shunt can't hold all those neg wires, then you need a neg buss for them and then a wire from it to the shunt and another from the shunt to the battery neg.
(Of course you will have a monitor now to keep track of your new batts)
The new two stage drops to 13.x once the batts are full? so no worries about long time 14.6.