If you make use of backplane relays or connect the DMM LO to the Output HI of bank 2, then you could measure between any two pins of bank 1 and bank 2.
If you have more than one 3723 card in the 3706A chassis, jumpering it to the backplane will be recommended way.
On rear of the 3706A is a DB15 connector that brings out the DMM HI and LO as well as the backplane relays HI and LO.
A small jumper on the DB15 could connect the DMM LO to the HI of backplane 3 (for example).
Each card (one by one) would need to close backplane #3 of MUX Bank 2 when a channel on that card is one of pins.
In the channel patterns, you can associate backplane relays with the card channel to have this automatic closure of the backplane relay with the channel.