I am curious about dialing in good sound myself, having just picked up a whole new rig, with which I'm still tinkering...but I can offer the following advice:
1. Before you change your eq levels, or any levels, write the settings you've got down. That way you won't "mess it up" irretrievably.
2. From what I've seen on the forums, generally it is advised you start with all eq levels "flat", so nothing is being added or cut from the signal. This id includes turning up your master volume and tone on your bass. Then if you'd like to shape the tone differently from how it sounds "flat", investigate what each knob/dial does to your sound as you increase or decrease from flat, one at a time, and return each to flat before investigating the next. After that I suppose see how they are in combination.
3. Jaco has a very distinct sound, and I suspect he may have his tone knob on his bass rather low, although this may not be the case. I'm sure there's a wealth of info out there on how to imitate his tone, more or less. But if you're trying to keep your bass' "unplugged" tone when amping up, you will have to try to minimize the effect of your gear, pickups, etc on the natural sound of the instrument, which will involve a bit of monkeying around and comparing back and forth.
4. Don't forget to make sure you're at playing volume (whatever that is for your situation) when you decide on a certain amp setup. Volume can make a big difference.
Good luck!