After you have uploaded Marlin you need to calibrate a few things, X Y Z and Extruder stepper motors and making sure the bed is level.
To calibrate the stepper motors see the video below, this video is for the Extruder however the same theory applies to the other stepper motors.
https://www.youtube.com/watch?v=w_Wb0i0-Qvo&list=FLsBw9MazlOn_-0v7O8OSgwg&index=7
For X and Y find a reference point on the side of the x carriage or front of the Y frame take a measurement to the extruder module or the front of the bed. Then in Pronterface of Repetier host move the axis by 50mm and then see how far the extruder module or the bed actually moves. Next, find you current E-steps in marlin under the configuration.h file and make a note.
Then use this equation (expected distance / actual distance) * current steps per mm = new steps.
so if I asked X to move 10mm and it only moved 7 I would do 10/2 = 5 then find my current steps per mm for the X axis and times it by 5.
This works for the Z axis as well.
Then enter the new E-steps into Marlin, upload and save. You can also alter the E-steps on a lcd and save to eprom if you have this enabled. On the LCD go to Control => Motion and scroll down to Xsteps, Ysteps, Zsteps and Esteps. Click on then and change the value accordingly. Then go back to the control menu and click save. This saves the steps for each axis.
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