Welcome to the forums! 
Z being "inverted" is normal - the Z control should control the space between the nozzle and the bed, regardless of which moves, right? You get used to it after a while. 
Have you 'homed' the axes yet? Often movement is prevented before homing has occurred. Try homing z, and see if you can move the full range.
At this stage, look up how to:
* Adjust the z-stop, and
* Level the bed
And after that there's plenty of other calibration you can run - I'd recommend reading through these forums, and note that much of what's written about the older printers (SD2,3,4) is likely still quite relevant to your workbench - for a start, maybe consider:
* Belt tensioning
* PID tuning
* Extruder calibration
* Wall-thickness calibration
Good luck, happy printing!
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi