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EQ before distortion - Fender Blackface, Boogie Mark Series etc - better for 'pushed cleans' and smooth lead sounds, each frequency overdrives separately to some degree. You don't usually want too much bass (farty) or treble (harsh) so it's all about the mids, and it tends to be more 'pick sensitive' to dynamics (ie altering picking changes tone more than volume).
EQ after distortion - Marshall, Mesa Rectifier, Soldano etc - better for crunch rhythm and scooped lead sounds, the whole signal is distorted first and then 'sculpted' by the EQ. You can turn the bass right up and scoop the mids if you want, and it tends to have more separation for chords and give 'volume' dynamics (ie altering picking changes volume more than tone).
Obviously that isn't always the whole story, there are other parts of the circuit that affect things as well, eg how many gain stages and their inbuilt fixed frequency responses, whether the tone stack is driven from the plate or cathode of a valve, etc.... and that in traditional amps, the power stage distortion is *always* after the EQ, so this is more to do with master volume amps. (Although some of the distortion in vintage Marshalls still comes from before the EQ.)
Does that make any sense?
How you should set them - how they sound good. No rules really. It is generally a good idea not to use too much gain and bass at the same time with a pre-distortion tone stack - but just experiment, you may like it.
The method of turning each tone control until you find the spot it does the most over the smallest turn range genuinely does seem to work as a quick way of getting at least close to the 'best' sound from an amp... usually.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
In short, I also think there's no easy way to predict how tone setting will sound in an amp without just trying it.
And... I'm not an expert so happy to be corrected on anything I've said!
The clean/crunch channel will be, anyway - the blues/burn one might be a halfway house like the Dual Caliber series, which has *both* - internally fixed pre-EQ, and controllable post-EQ, although plate-driven not cathode-driven so it still sounds nothing like a Marshall.
I did say it was sometimes more complicated .
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
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ICBM has covered it very well above, the other thing is that tone stacks are not all the same, so even a JTM45 tone stack compared to a JMP tone stack are quite different in how they sound, even though they are both placed at the same part of the circuit.
This also confirms what Hootsmon asked and I suspected from the sound, the EQ is pre-distortion on both channels. As is often the case with Mesas, the valve layout is rather odd too - V2 is the first valve on both channels, and the distortion occurs in V1 and V3A. (Possibly some in V2A - which is the second stage, and before the tone stack - at high gain levels, but the bulk will be from the later stages.)
The graphic EQ - Contour is the usual four-transistor circuit but with fixed values - is, like all Mesas, post-distortion.
(You know this of course, but for Hootsmon and others) the tone stack component values can make a huge difference, especially the treble cap and 'slope' resistor. Both are different on the JTM45 and the JMP Lead models, although the Bass and PA models retained the older values.
All this is part of what amp designers do to 'tweak' circuits and make them sound the way they want, which is why there are so many different amps and they all sound different even when they're really quite similar circuit-wise.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
Looking at the actual circuit schematic, it looks like:
Channel 1 - input > V2B > channel 1 tone stack > channel 1 gain control > V1B > main channel switch
Channel 2 - input > V2A > channel 2 gain control > V2B > channel 2 tone stack > V1A > main channel switch
But the reason for the even greater complexity around the gain controls is that V2A is *also* switched in when Crunch is selected on channel 1.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein