Consider the 'Q' knob again (or 'Q factor', or 'bandwidth', or whatever they've called it on your plug-in), you might want to broaden the bandwidth slightly so that it is cutting a slightly larger range of frequencies. Have a fiddle around with this parameter until you've found the sweet spot.
There might be more than one frequency you want to get rid of, so just repeat this process again. Sometimes, you might have a clump of frequencies in a similar area of the spectrum, such as the low mids, which are giving your tone a certain undesirable characteristic.
Too much prominence in the low mids could make your tone sound 'boxy', or slightly wooden and dull. Consider cutting a number of pinpointed offending frequencies from the low mids, or even just setting a wide bandwidth and cutting a large chunk.
So far, all I've talked about is cutting, and not boosting. Well generally, it's not the best idea to use EQ plugins to boost certain frequencies, because then the digital plugin begins to flavour your tone and leaves its signature all over your sound.
It also means you might be clipping the signal in certain places and increasing white noise.
If you have a good plugin though, or even an analog EQ rack unit, then it's not the end of the world, and to be honest, I've boosted frequencies using some pretty cheap EQ plugins, and I've managed to get some great sounds.
Working out which frequencies to boost can be done with the same 'notching method', but instead of trying to find offending frequencies, you're trying to find the ones which are struggling to be heard in the mix, and trying to give them a bit more prominence.
So as far as this feature goes, and for home recording, this is really all you need to know. But you can go so much further. Understanding EQ is the key to creating great mixes.
One useful trick is to find a frequency test on Youtube. This basically plays certain frequencies at you and you close your eyes and try and guess which frequency you are hearing.
For example, if somebody plays me a sine wave at 562Hz, I could probably estimate that it's between 500 and 600Hz, because I spent a serious amount of time (to the anger of my partner) doing frequency tests.
It's a really useful tool, because you'll be able to identify which frequency needs cutting from the hi-hat track, or which band of frequencies need a bit of TLC on the acoustic guitar track.
It also helps you identify pitches and notes on pianos or guitars, developing your musical ear.
Get to know EQ, get to love it. It's your best friend. You don't need fancy equipment or software to be good at EQing, you just need a good set of ears and a bit of logical thought (and a lot of practice).
Set value judgements aside. You might think that a certain amp or pedal 'sounds' great, or has a really nice mid-range characteristic. But if it isn't sounding comfortable in the mix, you need to set aside your value judgements, and rely fully on your ears to make it sit better.
But most of all, remember us motley lot here at Sonic are always around to help. So if you ever have a question, just get in touch with us on our Facebook page.