I own a axe fx, and it was one of the hardest things to tweak. Finally after a year i have this thing sounding amazing (to my standards at least)
Look at the axe wiki for tightening up bass, that step one
Add an amp four blocks in. Now i use the 5150 model as it works best for me. Turn the gain around 8 to start, on the treble knob, hit enter to engage the bright switch. Now you'll notice plenty of gain has been added. Set the eq to taste. Onto the next page, set presence to roughly noon to start. The damp control affects the tone drastically. too much and it sounds like static, but not enough and you won't have any highs (turning it off gives it a scooped feel). Set to taste. Play around with the presence and damp to get a nice high end, but don't add to much as you'll get static. The master should never go about 3, any higher and its use a muddy mess. Now here is the trickiest part, the last page. Go to town stack, select 5150, the change it to post. I found that around 500 the tone stack is the best starting position. Ok so you've gotten this far, and when you chug it the strings sound like shit, its too bright! Now i believe its the b+ value you want to change, set it to a very low value and you'll notice the brightness go away. Turn it up to a value thats bright, but not giving you that string slapping off of the board sound.
Alright, so add a cab to the right, and a cab underneath the cab you just added. set the cab and mic to your taste, and set the levels to taste also. If you still have a low ridden muddy mess, add a tube screamer before the filter, that is before the amp. Don't add any drive, Turn the tone knob to taste, and set the level so that it won't drive the amp to an insane amount of gain. Gain staging! On the eq portion of the drive pedal, turn down some bass, and add some mids around 1400.
last but not least, you still have some crappy low mids, add an eq and filter out the low end and high end, and take a notch out of 250 to 300 hertz.
Here you go, this is from personal experience from wanting to throw my axe fx out of the window. I hope this helps