Since you get an "E", it is a bad pot.  What model do you have?  Axsys 212 or AX2?  If you have the Axsys, the control knobs are in "capture" format which means you have to turn the knob to the assigned value before it will change.  If you have an AX2 chip (even if you have the Axsys chassis), the control knobs may be in "Instant Access" which means as soon as you start to turn a knob, it immediately moves to that value.  For example, maybe you have the drive knob set at 25, but the knob itself was in the 3 o'clock position.  As soon as you touch the knob to turn it, the amp automatically jumps to a drive value of 75.  I suspect your system is in Instant Access, so the bad pot(s) jumps between different values and makes a mess!  To check what chip you have, press the AUX/MIDI and MAIN buttons at the same time.  If you have the original Axsys it will show v1.04 or 5, AX2 will be 2.01 or 2.

Depending on the age of your model, to open it up, take out the screws on the handle, on the sides (usually two on each side) and any others on the top of the case.  Don't worry about the screws holding the metal corner protecters.  Once the chassis is out, remove the screws holding the removeable metal top plate (runs the length of the chassis).  Once in, you'll see the several ribbon connectors which you'll be unplugging when you remove the PC boards, so that will accomplish the unplug/plug portion.

To get to the pots (yes, they are the knobs that control tone settings) you'll have to take out the screws that hold the PC board to the chassis, pull off the knobs and take off the nuts that hold the pot stem to the front panel.  Replace the old pot with a replacement.  These are not "off the shelf" pots.  Thye have a longer stem than what you might find at radio shack, etc.  Call Line 6 service department and ask for the replacements.  I've had 5 of these amps over the past 8 years and they've been very good at sending me new pots.