...I'm gonna share my answer here (hope he don't mind), keep in mind that my opinion is no more valid than my pilot's license...which I don't have.
So, here, with out further ado (doo doo doo), is my screed on EQ, use it in good health, or laugh at it (which is supposed to be a healthy thing! 
):
Man, that is a HUGE topic, distilling it to a few paragraphs is difficult...maybe even
dangerous!
First, to clean up your understanding of how your preamp controls work (or at least what I am perceiving as your understanding - my apologies if I'm incorrect): The typical EQ control will cut and boost a specific frequency, not affect the actual frequency itself*, particularly on a bass' preamp, and usually on the amp itself. So turning that knob is not changing WHERE you are cutting and boosting, just how much you are. There is a bit more to this, not only the center frequency, but also the "Q" or bandwidth of how the control works. Some preamps will have a very narrow bandwidth, others a more broad one - this stuff gets a bit above my pay grade quickly, but typically most preamps have pre-set Q's, so we'll stick with that for now:
When you turn your EQ knobs on your bass, you are changing ONLY the cut or boost at a specific center frequency and the surrounding frequencies to a certain point.
Now, what do these things DO? Man, there's the million dollar question!
There is a lot of opinion out there, and my voice is just one in the cosmic fugue here, so keep that in mind.
I have a K.I.S.S. philosophy about most things in life, and here is a strong place for that to work.
Minimal changes. Start with everything on both your amp and bass FLAT. Then, use the AMP first to get as close to the tone you're hearing in your head as possible - your idea of a good "basic" tone.
Then, you can make variations for taste, and adjustments for situations with your onboard preamp.
The single most important tone knob you have, by the way, is your right hand. Before you touch anything else, play around with where you pluck and how you pluck, and see what that does with the tone.
Next, your blend control or balancing your dual volume controls (if you have a 2 pickup bass). You probably already know this, but you can TOTALLY change the character of your sound with even minimal changes here. Again, experiment a bit, you may find odd things - like favoring the neck pickup helping to cut through more than favoring the bridge. If one thing doesn't work, try the opposite!
Shoot, we haven't even talked about the preamp!
Here, to me, it's really true that a little goes a long way.
Rule one in my universe, NEVER CUT YOUR MIDS.
Ever.
Period.
I know how great it sounds to get that "scooped mids" tone sitting in a music store or your bedroom playing solo (I almost said "playing with yourself"...oops, I did
). That tone is DEATH in a mix. If you can't hear a bassist at a gig, check his EQ, betcha you'll find a "smiley face" or it's equivalent somewhere in his signal chain.
Boosting highs and lows and leaving the mid "flat" is not a way to avoid this rule, by the way - it gives the same affect: no balls.
Balls = 200-250 Hz. Guitar (standard tuned) bottoms out at 300 Hz; bass drums are usually around 80-120 Hz. That leave a great big HOLE in the mix for US, if we decide to use it (and the keyboardist stays out of our register. If he doesn't, it is legal in most states to shoot him.
). Use it. Low-ish mids are your friend - yes they sound like POOP soloed, but man, with your buddies blazing away all around you onstage, they sound FABULOUS!
My take on using your preamp is simple, fix room problems like too much BOOM (hey, cut my lows) or CLANK! (hey, cut my highs); getting a particular tone for a tune or part of a tune (slap solo - crank the mids a bit [serious, try it sometime!]) - not for creating your basic tone. Adjusting your tone for the situation.
In the end, I didn't learn from books, I learned from doing. I used to live in Orlando, and ran into all the "book smart audio engineers" that were pooted out of the street-side orifice of Full Sail, and frankly, they were useless - lots of theory (which absolutely has it's place!), not a clue how to apply any of it. I swear getting that "education" made them worse, not better. Try stuff, foul up, make fart sounds - remember 'em, that way you can avoid 'em when you need to, and get 'em what you want 'em!
*Parametric EQ's, which are fairly rare come in two flavors: 1) semi-parametric, which allow you to cut and boost and vary the frequency that you do it to; 2) fully parametric, which allow you to adjust all three parameters - frequency center, Q, and cut/boost. The only thing like this I've ever seen on an onboard preamp is the EMG BQC preamp, which has a semi-parametric mid control. Your amp may have semi-parametric (Eden for example typically will have 3 bands of it, plus "shelving" bass and treble) or a band of fully parametric (Demeter HBP-1 has a single fully parametric control that can be switched in or out). My take: more controls = more opportunities to #$^ up.
Good luck!
