Hej
I think this is what I am trying to figure out. I know that it will all come down to my ears in the end. But I would like some knowledge on where/how to adjust EQ instead of doing things randomly and hope for the best.
There is no single answer because each piece of gear has it's own unique character. You need to gain intimate knowledge of your amp, speaker, and bass in order to make the best choice. Also as I said earlier, you need to understand how your gear works, so you know the consequences of your choices.
I have a fairly large collection of amps. The natural voice of some of them is very close to what I like. Also some of them have very powerful tone controls, so the can easily be adjusted to produce a wide range of sounds. I can pretty much run the bass flat with these amps.
Other amps in my collection have a baked in tone that is not as close to what I like and the tone controls are not powerful or flexible enough to always give me the sound I want. I would be more likely to use my bass's tone controls with this type of amp...or perhaps and separate EQ pedal.
You might ask why I keep amps that I don't like. Actually, I do like them as they have a unique voice that I cannot be produced with my other amps. Sometimes I am in the mood for something a little different, and I think it's very cool to have a bit of variety.
So unfortunately the best advice really is plug in and fiddle with the knobs until it sounds good. Try to learn the range of sounds you can get with each control on your bass, amp, and speaker. Then when possible, use the controls that only impact the sound you hear, rather than altering the DI signal that will be used by the audio tech.