The "knocking noise" is usually when the stepper motor from the extruder is blocked. This can have several reasons:

1) nozzle temperature too low, so the filament is not viscous enough.
2) clearance between nozzle and bed too small, so the pressure become too high inside the nozzle.
3) extruded volume is too high or too low (Yes it sounds a bit strange but there is also a minimum volume).

If you change to manual calibration (what I would highly recommend) you will also need to switch off the z-autolevel in the firmware or at least remove the stored values by sending M322 (Reset autolevel matrix) to the printer. Otherwise the z-axis will do some unwanted micromovements. https://github.com/luc-github/Repetier- … issues/145.

He mentioned being a newbie, and Simplify3D supports the 1.0. There's no reason to believe he's using Repetier or any autoleveling.
He likely used the built in calibration function to level the bed with the screws, which doesn't do autoleveling like other printers. Yes, he should just use the manual calibration of folded paper thickness, but that's mainly for ease of calibration, not for autolevel compensation.

If the extruder is pushing out plastic, then you're good on that end. The knocking could be a consequence of retraction being enabled. It can cause a knock. If your prints are coming out fine, but you hear a knock, I wouldn't worry about it.

1) nozzle temperature too low, so the filament is not viscous enough.
2) clearance between nozzle and bed too small, so the pressure become too high inside the nozzle.
3) extruded volume is too high or too low (Yes it sounds a bit strange but there is also a minimum volume).

If you change to manual calibration (what I would highly recommend) you will also need to switch off the z-autolevel in the firmware or at least remove the stored values by sending M322 (Reset autolevel matrix) to the printer. Otherwise the z-axis will do some unwanted micromovements. https://github.com/luc-github/Repetier- … issues/145.

The auto calibrate is crap. just get it to pass then never use the auto calibrate again use the manual way