Go to machsupport.com and check out the video tutorials. They are great and answer 90% of the setup questions.
Re your encoders, they are quad which means X4. So, 1000 (250 X 4) X 5 revs per inch (.2 screws) X 2 (gearing ratio) = 10000 steps per inch!!! Someone correct me on this if I'm off!!!
Re. limit switch drive, there is a command on the settings screen (I think that's where it is) that turns on the automatic drive off!!! But, it's all in the videos. Mach is great!!!