Caveat: I’ve been playing for a few decades, but I am *not* an engineer or a physicist or even anywhere close to being a scientist.
With that caveat, here’s some of my theoretical understanding of EQ, versus some of the more practical/tactical knowledge shared in this thread. Hope it’s helpful for OP or someone else. Also I’m definitely open for correction!
When a lot of people say tone, they mean timbre.
The frequency of a note by itself is just a sine wave, like that tinnitus ringing in your ear sound. What gives an instrument its unique voice is the accumulation of harmonics that are also heard when a note is played or sung. Some of those harmonics will be naturally boosted or cut or sustained or dampened depending on resonance. That gives an instrument its timbre, and what makes your spoken voice different from mine.
(I’m using the term harmonic here, but some of those additional frequencies are also disharmonic. Ignore that for now.)
When you make EQ changes, it’s important to understand that the change affects primarily that frequency, eg. 50 Hz. In addition to that frequency, there are nearby frequencies - 40, 43, 52, etc - that also get affected. This range is the width, literally the band width. If you boost, imagine you’re building a mountain with the peak being that frequency the slider is set for. The width of the base of the mountain is the bandwidth. Similarly, if you cut, you’re making a depression, and the width of the top of that depression is the bandwidth.
Imagine an X-Y axis, where Y is amplitude of signal and X is frequency of signal. Y is what you’re controlling when you make a change with the slider, and X is the slider itself.
So given that each note played or sung is a package containing the fundamental frequency as well as an assortment of harmonic frequencies, when you boost or cut in a given band you are only affecting the frequencies in that given band. This is why when you cut at 40 Hz you’ll still hear the low E, but what you’re primarily hearing is the package of harmonics that exist at higher frequencies, and they inform your brain that a low E is being played. It also means that if you have a high frequency band boosted, you’ll still hear finger on string noise or fret buzz when playing those low notes. Boosting a band will not affect the amplitude of frequencies outside of that band, but may result in them being “shouted down,” lost in the relative amplitude of that band.
Many of these extra frequencies live in the mid range, so making changes to he mids can have a big impact on your tone. A scooped setting (lowered mids) can sound more “pure” when played without other instruments in the mix, and we hear that as good and musical, whereas boosted mids can sound honky and nasal when played solo.
In a mix however, those midrange bands are where the bulk of your “tone” (timbre) actually reside. And given that a guitar is typically an octave higher than a bass, their harmonic packages per note will be other than yours, so boosting the mids in a mix allows you to cut through more, be more audible in the mix. Some of those frequencies are washed over or played with more amplitude by other instruments, so what you tend to get more with a mids boost in a mix is much closer to the timbre of your instrument, versus that honky nasal quality.
Overdrive/distortion/fuzz basically add more harmonic content and/or drive higher the amplitude of ranges of harmonic content. Putting an EQ before any of these or before a preamp and boosting a given band will overdrive that band going into the pedal/preamp circuit, so can give you more of that white noise around that that band than you otherwise would have had. Having an EQ before or after one of these pedals will have different effects.
It’s important to understand that settings for one combo of bass+pedals+amp may be very different when used with another bass or pedal or amp.
Compression typically affects a note in both amplitude and sustain of harmonic/fundamental frequencies, raising the amplitude of the quieter ones and lowering the amplitude of the louder ones. When you first attack a note, with your finger, your pick, your thumb, etc, that initial note attack has a higher amplitude of many of those frequencies, and then they decay (lose sustain) over differing periods of time, depending on the structure of your bass and the natural EQ of your signal chain. Sustain basically means they maintain a given amplitude longer. Playing around with a compressor, you can lessen or increase that attack, add sustain, or reduce sustain. Having an EQ before or after a compressor will also have different effects.
So where an EQ is in your signal chain is important. The one on your amp is post-preamp, one in your effects loop will come after the amp’s EQ, and you can place one at the very start of your signal chain, right out of your bass. Playing around with an EQ pedal’s location is also important to spend some time with.