As a general rule, most musicians (especially guitar players) have no idea how to use anything that adjusts the frequency bands of their instrument, meaning the amplifier tone controls.
The reason is that they're never taught what tone controls are there for, and there's not a lot of information in the manuals that comes with amplifiers either (if anyone actually reads them).
This excerpt from the Ultimate Guitar Tone Handbook shows the 3 general reasons to use the amplifier EQ.
1) Many stringed instruments (like bass and guitar) have dead spots on the neck where a few notes can drop in level. A bit of EQing can help smooth things out if you can zero in on the frequency band of the notes that are dropping out.
2) You need to compensate for a frequency range deficiency. This could mean a situation where a Strat might not have enough bottom when played through a Marshall Jubilee so you’d add some low end with the tone controls to compensate. On the other hand, a Les Paul through the same amp might be too bottom heavy so you’d subtract some bottom. And then that same Strat might just have a mid-range that’s like an ice pick through the eardrums on certain notes, so you’d back off on the mid-range a bit and pull the pick out of the ears.
3) And finally, to keep the instruments from clashing in a scenario where 2 players use the same model instruments and amplifiers (like two Les Paul into two Marshalls). In order to fit well together frequency-wise, one player would adjust his tone to have a bit more bottom and maybe scoop out the lower midrange while the other player would go for more top end with a midrange peak just where the other guy scooped it out. There you have it - instant blend.
Of course things are never quite that easy in real life. Most guitar players never get to audio nirvana with their sound in the first place (it's like finding the perfect wave - it's out there but rarely experienced), and once found, it's difficult to get them to deviate from anything they’re comfortable with, even if it makes the band sound better. But if a player hears how successful the above techniques work in a controlled environment like the studio, they’re usually a bit more open to experimentation afterwards. Of course you can always tell them that xxx (fill in their favorite artist) does it that way to get his or her attention, because he probably does.
Whatever the method used, a judicious use of the amplifier tone controls can make a huge difference in how a band blends together both on-stage and in the studio.