It all depends on what you are trying to do. First, though, is it a TRS (probably), or a TS?

Will you be running some balanced, and some unbalanced?

Are there any units that you normally run in series, with very few instances of needing to interrupt the signal to run through something else? In other words, do you want to run the output(s) of one device to, say, in on module 12 to be normally connected to the input(s) of the next device through module 12 so that it's always connected, unless you choose to insert something else?

Or, do you want complete separation of all ins and outs so you have to use cables to run any output into any other input?

Most patchbays can have their modules flipped, or otherwise configured, to provide normalled, half-normalled or non-normalled access from the front. You have to determine if you want it one way or the other, or a combination. That depends on what you want to do.

You should probably start by drawing yourself a flowchart of the system, and deciding if you want any signals fed serially through the patchbay, or separately for each in and out. (You'll save space if you run some serially, but may need access at some point).

If you know for CERTAIN that you'll ALWAYS run this output(s) to that input(s), do yourself a favor and wire them directly with one cable. You'll minimize possible confusion, and you'll minimize possible failure points in the patchbay contacts, or by using more cables. You'll also minimize more possible instances for noise or signal degradation to occur.

In my effects racks, I have installed my outboard effects (preamps, EQs, compressors, multi-effects, etc.) top to bottom, in the most logical order that the signal may travel, with the top unit starting at the left of the patchbay. It makes it easier to say "OK, I'm using the 3rd down, so I immediately know to go to I/O 5 and 6 on the patchbay, even though I have made printed out charts to refer to. (Do yourself another favor and download/create a patchbay chart to type in all the inputs and outputs.

Also, since I have some funky old "prosumer" gear that I run through occasionally, I created a "Notes" section on each chart to list the operating characteristics of each, such as "Bal, +4/-10 (switch) or UnBal, +4/-10 (switch)"...etc., to remind me what each unit's characteristics are, and how it's currently set so I'll know how to deal with interconnections between Bal/UnBal and +4/-10. (That patchbay is labelled on the chart as "Neutrik Patchbay (Rack 2) Non-Normalled", just to keep things straight.)

So, start by mapping out your system, and deciding what you need access to, and how you want that access handled. Then, decide how you want your patchbay configured so you can make any adjustments before you start plugging in a bunch of cables. Then, make a chart and print it out so you can follow it while connecting.

Then, when you are all connected, test everything out.

If everything works, and you have no weird noises or ground loops, etc., then start working with it.

After you've worked with your first attempt for a while, and you find out you really SHOULD have done THAT like THIS, rip it all apart in frustration, and start all over. After another try, or two, you'll have it just like you want it.

Until you buy another piece of equipment.

Good luck,

Kapt.Krunch

You bring up some good points
Most of which I have pre thought about such as some routing, dedicated "hard wired" gear, charting the cables and connections.
First:
I track mostly in line, rarely do mic'ed tracking.
Right now I have Neutrik TRS patchbays (modules change via a quik flip) plus one TS patchbay ( switchable ), which I am trying to incorporate into the maze.
The Neutrik unfortunately did not have any optional switching contacts which would have helped, I may get a couple of those modules.
Most of the F/x gear is used on alot of different instruments so they would be NOT hard wired.
Really there is nothing that would be direct wired. As I try to stay very flexible to processing certain instruments i.e. drums etc individually -
I do alot of Soundtrack and Ambient Space, some Chill to give you an idea.
The SPX 90 ,1st gen, in use is unbalanced that is the only kink in the works: that unit to receive a balanced signal then to run an unbalanced signal into a balanced patch bay. Would I have to convert signal to an unbalanced one for this unit ? or go right in to it.
I am seeing something like this perhaps:

Pbay #1= instrument outputs, Interface DAW inputs, Mixer inputs.

Pbay #2= F/x, Comp Limiters, processors in's+out's