well how do you want it to stand out in the mix....do you want it boomy...or do you want it to sound dry as if it were just a lower tone guitar....or what have you.

details my friend...DETAILS!

Dry. I don't want to have to have a subwoofer to hear it. I'd like to get a nice woody sound out of it within the mix. Should I maybe double it up and make one track extremely low and then use the other one to clear up to the tone?

I usually use a high pass filter up to a low mid frequency, then that goes into some light compression. Then I EQ out a little more in the middle (-3 to -6) with a wide Q (2.0?), and add another high pass filter at the end cut up to taste with the reso control up a bit to give it it's low mid punch back. Hopefully since you're cutting, you won't have to boost anything, but if you do I'd say another +3 at around 3k also with a decent Q.

That's how I record my viola bass. They're tricky cause they have tons of sub, a lot of attack, and are hard to get definition out of without having excessive midrange. That bass and that amp shouldn't give you very much trouble though. :) I think the trick is to cut some low mids to let some articulation through... atleast that's what works for me.

Is the amp in a corner?

If your mixes are really thick and full sounding at the end product, then try shooting for a slightly thinner bass sound.
Usually I bring out some of the high end clank of the bass when I record it, because otherwise his playing is inaudible in the mix, and if I turn it up, it overpowers the mix.
Maybe duplicate the track and add some really gritty distortion to it, then blend the tracks together?

Of course that kind of sound may not be what you're aiming for, but it does the job for me, and I don't have a sub hooked up the speakers I use when I mix and master.

When I listen back on other speaker systems, it usually sounds full enough AND clear enough.

Don't be afraid to add a healthy amount of compression either, want that low end to be nice and even throughout the song!

Take my words with a grain of salt. I'm a bit of a newbie who records his band in his bedroom with very limited equipment (VSTi Drum Program, a Peavey 5150, an SM57 and an AKG Perception 200), but after a short amount of time playing with the settings, I end up with a bass that stands out without being irritating.

Note that when Paul McCartney wanted his Hofner to stand out in the mix he switched to a Rickenbacker. That's mostly a joke. I like the sound of a Hofner, but you shouldn't try to make it sound like something it's not. Listen to McCartney's Hofner on Let It Be - Naked. (Ignore John and George on Fender Bass VI on the songs where Paul plays piano.) I think it's a great job of letting the Hofner sound like a Hofner, but getting it to sit well in the mix.

What kind of DI's or vocal preamps do you have? Taking it direct may be a better way to go. And I agree with BrianW that an Eq curve with high and low cuts and bumps in the low mids and about 3k works with a lot of basses in a lot of mixes. (YMMV, there is no one-size-fits-all eq curve.)

Does your bass sound good when its solo'ed? Is it only when its in the mix that you have problems? If so the problem might be everything else.

Stick an EQ on your bass and experiment with boosting frequencies: try to identify a couple of important frequencies that are integral to the sound you are after... these might be 80Hz for the low weight and 200Hz for the warm fatness, or you might decide that the 500Hz region is where the 'woodiness' you are after lives... then bypass the EQ, and experiment with cutting those same frequencies out of other elements of the mix, eg: highpass filter your guitars at 100Hz to allow the 80Hz region of the bass room to breathe, or notch out 500Hz from the keys to let the woodiness of the bass through.

A good mix should fit together like a jigsaw puzzle, with every important element of the mix sitting in its own little sonic space...

Thanks everyone this is really helping. IIRs, I tried pretty much what you said, and that seems to work the best. It seems so obvious to me now, you can't have too much in one place. As for DI, I don't really have a great option for that right now, and I actually do love my set up right now. It sounds pretty damn good solo'ed. I also ended up putting on a leveler instead of a compressor, I just couldn't get the right tone without distorting it first. Brianna, The amp isn't in a corner, but its in a 6x6 closet. I ts sound treated, and I love it for guitar amps and vocals, but could that be deadening my sound too much? I tried doing my acoustic instruments and there and I just couldn't take it. I'd rather have some room reverb that I have to deal with rather than having my instruments to sound like they've got a towel inside them.

ya dude, just experiment. im not sure how it all sounds but with me i usually use a HPF to cut out the boomy-ness that muddies up the mix then compress it a bit to round out the sound. then tweak the middle and high frequencies to where i like them.

but DI AND mic the bass and you can pick and choose or mix between the two to your liking and such.

just have fun man effing around with ur shhhtuff!