Plumbing Your Pedal Board
I thought I'd address a topic that I get asked about quite a bit on the layout and order of effects within your signal chain.
I should say before we dive in, there really are no hard and fast rules here. Ultimately what sounds best to you is what is best and sometimes the unconventional recipes can sound amazing so it pays to experiment - and besides it's fun to try new things, so go for it!
Think of your signal chain working much like the plumbing in a house - there are wide pipes and narrow pipes that your signal has to pass through before it hits the amp. Each pedal has specific characteristics that help to determine its 'width' - its EQ parameters, compression level, headroom before additional clipping occurs, and output level.
For example, an overdrive with a simple treble roll-off tone control and a decent amount of compression would be considered a 'narrow pipe' using our analogy; an OD with a more complex EQ sporting separate controls for different bandwidths and very little compression would classify as a 'wide pipe'. Once you've determined the width characteristics of your individual pedals you can then tailor just how wide or narrow your frequency spread remains along your entire chain of pedals when you're setting up your board.
If you're a player who likes a lot of dynamics and a big EQ spread, running the 'narrow pipe' type pedals into the 'wide pipe' pedals helps to preserve the dynamic content by keeping compression and additional unwanted clipping to a minimum, the signal can breathe more and it allows for a fuller, more widespread EQ field with increased clarity. Players who use their guitar's controls should find it easier to clean up their fuzzes and overdrives using this methodology when the pedals are used in combination. If you were looking to get very focused and saturated tones, reversing the order from wide into narrow would be the better choice due to the increased compression that occurs when you push a lower headroom or simple tone stack pedal further into overdrive with one that has a wider frequency spread and greater dynamic content. Your signal should have a tighter focus with a more pronounced frequency cut this way and may be the better path to choose if you want to stand out in a busy mix.
I thought it might be helpful to break down what I think are the three most common pedal groupings in a typical multi-pedal set-up and explain why the placement of certain pedals in particular sections of the signal path can have positive or negative consequences. Again, these are only examples and shouldn't be considered the only way of doing things, experiment!
There are certain pedals that typically do best at or near the very front of your signal chain. Most Germanium and Silicon-based fuzzes, treble boosters, octave generating effects, and input-sensitive devices like oscillators, envelope filters, or Uni-Vibes for example perform to their greatest potential by getting a clean signal directly from your pickups - certain wahs do too for that matter. A buffered pedal or active pickups in front of any of these devices can sometimes mess with their dynamic response and overall tone, so if you use one of these pedals its prudent to experiment with buffer placement to hear what if any effect you notice on dynamics, feel, and EQing. If you are a player that incorporates a lot of guitar volume manipulation in their playing technique to get a variety of sounds from your rig you will likely notice significant differences when the buffer is placed after those pedals versus having it prior to them.
A quick side note re: buffers
There's a lot of mystery and misinformation surrounding their use and it can be hard to know who or what to believe. What is true is that they affect how your signal responds dynamically and that they restore lost high frequencies that can be dulled when running long lengths of cabling or a whole bunch of true-bypass effects pedals. What is false is the belief that they are all bad. Knowing what effect they will have on your overall tone can really only be learned by experimenting with one and seeing if you need one or not.
Less picky boxes
Most overdrives and distortions can go anywhere, and by applying the 'plumbing' analogy described above this is where you can begin to sculpt the dynamic response of your dirty tones and explore different 'stacking' combinations if you have multiple drives on your board for EQing shifts or additional gain. Play around with different orders and note the differences, seemingly simple changes can be pretty dramatic!
Where you place a clean boost is best determined by what outcome you are trying to achieve by using it. If the goal is to get a mild volume jump and additional compression or saturation for lead work for example, placing it before your rhythm dirt pedal is the best place for it. If you are looking for a global volume boost (aka the MORE! pedal), put it at the very end of your chain of effects before it hits the amp.
We're talking phasers, flangers, chorus, reverbs, delays, tremolos, etc. There are almost as many opinions on where they should go in the chain as there are pedals available and honestly it's such a personal thing to each user that it's silly to say what the 'correct' spot is for them. And I haven't even mentioned effects loops, that's a whole 'nother bucket of worms that I won't dig into here. But a lot of the stuff I've talked about previously can apply to mod pedals too, they have 'widths' like any other pedal and can have dramatic effects on the EQing and dynamics of pedals downstream from them so it's important to consider their placement as well when dialing in the dynamic response of your rig.
Wide Pipe Method
Here's a sample board laid out as an example that follows the 'wide pipe' signal chain method:
You'll notice in this example that the Naga Viper is first because it is a very dynamically sensitive pedal and I use it to boost the Fn5 and RAH (or both when I've had a bad day lol). Fn5 comes next because I sometimes use it to boost the RAH for higher gain sounds, the tone stays huge because the RAH's EQ spread is wide enough to accommodate the Fn5's girth. The Pareidolia is third in line to keep a wide frequency spread and more pronounced EQ shifting effect happening when used with the previous two dirt boxes, personal preference here. The RAH is my base dirt tone and gets boosted by everything upstream of it for higher gain sounds. The buffered tuner is after the overdrives in this case because I didn't like the effect it had on my guitar volume dynamics when placed before them. The Montavillian is after the drives to maintain clarity and dynamics. The SCP is last in the chain because I like to use it as a global volume boost.
Narrow Pipe Method
Here's an example of a 'narrow pipe' board layout:
The Perseus is SUPER sensitive to input manipulation so I want it first to get all I can out of it. Teaser Stallion is also input sensitive but to a lesser degree so it comes next. Both are used at times in conjunction with the WIIO which has the ability to either focus or widen the EQ spread via its EQ controls. The Manx is next, it likes being boosted by any of the pedals upstream for ridiculous amounts of gain and saturation. Tuner is next, but it could be placed in front of the Manx as it's not terribly picky about buffers to my ears. Semaphore is last because I want the hardest chop possible from it when running this set-up. I hope these suggestions inspire you to experiment and help you to get the most out of your gear, now go play some music!