Oh, one thing I forgot to mention is that it also makes a difference where you place the EQ. Since you got a multi effects unit I assume you use the EQ in front of them amp, but I will still add these thoughts, cause it is always good to realize the difference.
I believe most people place EQs in the effects loop and that with good reason. There you can really do what was described, finetuning the amps EQ.
You can however also place it in front of them amp (which I do most of the time cause both my Orange TT and HTH amp 5w Fender have no effects loop, only my H&K combo has one, but I personally like it generally a bit more). It still fine tunes the amps EQ, but in a different way, cause you also shape the distortion coming from the preamp tubes.
If I give a boost @ 1-2k Hz I not only directly boost these but also their corresponding overtones. Boosting about 250-500Hz gives me a bit more growl in the distortion. Also I can cut out 31 and 62 Hz (or even a tad higher) when using my heavy LP style axe with AMs in drop A#, cause they are just too much to handle for the TT imho (after all it is only 15W and cleaning up the bottom end like this greatly helps the clarity and the sound is still crushing as all hell).
I only do very small changes most of the time, as I do not wanne change the PUs tone much, after all I like them, it is just a little optimisation for each axe without changing anything else in the chain. Quick and easy to do for me.
I advice on also trying those two positions in the effects chain at some point, they are different in effect, really just a matter of taste.