Megatronics V3.0 3D Printer Board

The Megatronics V3.0 is the latest version of open source 3d printer electronics, designed to be a single PCB solution. The usual approach in the beginning of RepRap development was to use an Arduino board, and hook it up with a shield of sorts, which then interfaced with the printer's components. However most of the newer electronic designs tend to have the Atmega chip on board.
1. Plug in the stepper drivers (the extruder stepper driver goes into the E0MOT header). Be very careful when doing that, if inserted improperly they will most probably be destroyed when powered on. The proper orientation of the drivers is described in the Quick Start guide (you have to be sure the Vmot pin is at the right place). Also, note the three jumpers that set microstepping modes. You need to consult the chart for your stepper driver model and adjust the jumpers accordingly. (L or Low means disconnected, H or High means connected.)
Here is the chart for A4988 based drivers:
And here is one for DRV8825 based ones:
Your extruder and X and Y axes should be set to 1/16 microstepping, and the Z axis to 1/8.
2. Connect the motors. In case your motors (like mine) don't have the appropriate female connectors, you will have to buy some, taking care to connect the wires to them in the proper order, as shown below.
3. Connect the endstops, I only used the Xmin, Ymin and Zmin, since the max values are defined in the firmware anyway and I never use the max endstops. The endstop connectors have three pins for using optical or hall endstops, but since I have the stock mechanical ones, I only had two leads, which should be connected to the "S" and "-" pins (the "+" pin is not used).
4. The Megatronics board has 2 outputs for the print head fans. I only use one so I plugged it in the FAN1 socket, just beside the E0MOT stepper driver.
5. Plug in your hotend thermistor or thermocouple into the appropriate port (T0 for a thermistor or S1 for a thermocouple). I've switched from using UM's thermocouple to standard thermistors a while ago since the little amplifier board always got in the way of my designs somehow. Anyway, even if you are using a thermocouple you don't need that board anymore, just connect it to the S1 input. (Bear in mind that I don't know how well that would work since I have not tried, and I'm not sure if there will be too much interference from things like the printhead fan to use the thermocouple at all).
6. If you have a heated bed, connect its thermistor to T1.
7. Connect your heated bed to the "HB" terminals.
AFAIK, most Mk2 heated beds don't care for polarity, but others might, so take care.
8. Connect your hot end heater to the "E0" terminal.
9. Connect two 12 V outputs from your PSU to the "PWR" and "HBIN" terminals minding the polarity.
10. Check everything is connected properly.
11. Check again.

Usefully review and tutorial on Megatronics V3.0 please refer to http://www.chopmeister.com/2014/04/megatronics-v30-um-tutorial-review.html?m=1