For the previous iteration of this board I just used the tuner in the HXS (which is plenty accurate), but I wanted to be able to have a visible tuner that could be "always on" (mostly for peace of mind when playing arco passages when I can't hear myself well enough). It takes up an extra block, but I also add a mute block to tune silently.
I think your plan for the routing makes sense. Electric bass signal chain into the L input and upright into the R (and out to the Walrus DI/LI the same way).
I chose to run everything into the HXS and then use a block to add the Cali76 to electric patches to give some wet/dry mix flexibility (beyond the pedal itself). I made what's essentially just an insert cable to send two lines from the 'stereo send' on the right side of the HXS (I don't use any stereo effects so I tend to think of 'stereo' as 'dual mono'); into the INs on each external pedal and mono returns back to the HXS (in my case, I didn't bother running a return from the tuner).
It might be more cumbersome, but sometimes I like the challenge of finding a solution to a problem I created