Well, this was perfect timing for me. I was about to post a topic about this very set of questions to see what others were doing on their pedal setups. I just came to the conclusion for myself that I will be essentially isolating the real noise generating pedals in my setup. Speaking of which I will give a little overview, I am still waiting on some parts/pieces (also note that I play guitar as well, so my board config needs to pull double duty for bass and guitar):
Pedals:
TC Electronic Polytune2 Mini
TC Electronic SpectraComp
XTS Atomic Overdrive
ZVex Fuzz Factory 7
TC Electronic Croma Chorus Mini
TC Electronic Vortex Flanger Mini
TC Electronic Flashback Delay
Eventide H9 Max
Eventide H9 Core (but upgraded to Max since I own one)
TC Electronic Sentry Noise Gate
Morley Mini Volume
Ernie Ball 25k VP Jr Volume/Expression
Switchers:
Boss ES-8
G-Lab M4L (4 x midi controlled loops)
After a lot of consideration, I have decided to put my OD and Fuzz pedals onto the M4L which is connected to the ES-8 on one of the loops via the effects loop on the Sentry Noise Gate. This also gives me the room I wanted to put in a more clean/pure overdrive (as opposed to just the colored Atomic Overdrive). The ordering within the overdrives/fuzz pedals does not need to really be changed (i.e. I will have the clean overdrive first in the circuit, then the more dirty overdrive, followed last by fuzz). And I can not think of any reason to do it differently which results in any kind of useful sound when enabling multiple of this type of pedal (possibly the only exception being a parallel loop with a blending two of the pedals, but I have never needed that before...). As such, isolating the noisy pedals onto its own little group all of which are protected behind a very good noise gate to take care of any buzz (especially from some of the Fuzz Factory 7 settings), I feel I have a much better signal path throughout the system. And with the midi functionality of the ES-8 combined with the M4L, I can still control exactly which overdrives/fuzz are on or off at the push of a single switch.
I think the only other pedal I want to add (other than the previously mentioned clean overdrive) would be a Strymon Big Sky, since there is almost always some kind of reverb that enhances just about everything, and that free's up one of the H9's from always being used to pull that duty. Sorry no pics yet, as I am waiting on the M4L as well as a pedal board to put these all on (I have a PedalPad on order and then have the fun task of placing/measuring/cutting/heatshrinking/soldering custom length patch cables...).
Lots of digital pedals in that list, how are you powering it all? I've found that some can be managed on a daisy chain while others get horrendous noise if not on an isolated outlet