This seems to be the hardest thing for me to do. Cuase it feels like no matter how I record or compress/EQ the bass I still get wolftones popping out at me.
"Wolf tones" are a sympathetic resonance happening in your instrument at certain notes that creates unwanted overtones, and there's nothing you can do about that with EQ or compression.
If you mean a flubby, muddy sound or dynamic spikes from the bass, then that's all about EQ and compression. The reason to split a recorded bass tone in two (DI and amped tracks) is to leave the low frequencies (<200 hz) to the clean DI track and compress the hell out of it to get rid of the dynamic spikes that will pop out of nowhere. The amped track takes the higher frequencies (>200 hz) and gives you the body and grit of the bass tone. Applying amping to the low frequencies just gives you mud.
It's similar to how audiophiles will use a bi-amped stereo system, with different amps taking care of the low and high frequencies. The key is setting the correct crossover point between the two. I use 200 hz, but you should probably experiment in a mix to see where the sweet spot is.
The other thing that contributes to muddiness is a frequency pile-up between the bass, the kick drum, and the lower end of guitars. You'll want to carve out space for each of these with careful EQing, and there are plenty of tutorials out there on how to start doing that (though your ears will always be the decider).
I hate to say it, too, but good bass technique can reduce the need for compression. A good bassist can get a more even volume from each note, whereas all of us wannabe Steve Harris and Geddy Lee types out there whacking the hell out of the strings create wild dynamic swings that need to be heavily tamed with compression.
Also, are you recording with a fresh set of strings? Being a recording bassist is *expensive*, unless you want to sound like James Jamerson, as strings lose their brightness and edge very quickly. Gigging bassists love strings that have some wear on them, but they suck for recording.