I tend to agree with
@Ron_R. However, a Parametric EQ before the amp can do wonders. I use one for a set of Sheptone Tribute 4 Humbuckers. They are an emulation of A2 Humbuckers but with an A4 magnet. With the Tribute 4 pickup, bass and low mids can be woofy, the high mids can be lacking and the extreme highs can be spikey. I only used it with Canabis Rex speakers in the before-analog-times, primarily because of spikiness. A PEQ completely changed that situation for me with the FM3. I simply add the PEQ in before the amp, and most pedals, on any preset. It is in my PEQ block library now. My method is this:
Type 1 = Blocking; Frequency 1 = 35 Hz; Slope 1 = 12 db
This helps to get rid of the low rumble/energy sink part of the sound.
Type 2 = Peaking; Frequency 2 = 250 Hz; Gain 2 = - 9.5 db; Q2 = 0.68
This puts a mid valley in the same place that the Mesa Fat switch does.
It cuts and controls the wooly, woofy part of the sound.
Type 3 = Peaking; Frequency 3 = 800 Hz; Gain 3 = 5.4 db; Q3 = 1.1
This produces a nice mid bump -- to make up for this particular pickup.
Sometimes the gain might be set at 0 -- or even a cut.
It depends on the sound I am trying to achieve.
Type 4 = Peaking; Frequency 4 = 1550 Hz; Gain 4 = 0 db; Q4 = 0.7
I use this to fine-tune the upper mids.
Sometimes, I add gain. Sometimes, I cut. Usually, it is at 0.
Type 5 = Peaking 2; Frequency 5 = 3550 Hz; Gain 5 = -14.7 db; Q5 = 5.9
This last filter is particular to the Sheptone Tribute 4 pickup.
I use the last, 5th, filter to cut any squeaks, whistles or annoying high frequency sounds.
Set the peak to the highest gain and than sweep the upper frequencies for hateful sounds.
Once you find them, cut the gain as much as necessary.
This allows me to keep the nicer high frequencies and still get rid of the annoying part.
I have also found that this allows me to set the amp's controls for the best tone and feel.
I don't have to compromise the amp's sound to fix what is lacking in the pickup.
This is a good starting point. I think 250, 800, and 1550 Hz
are particularly useful points to adjust around.
But, there are no rules. Adjust to taste.
Start with these numbers and then see what works best for you.
I hope this helps.