Here is a picture of my test set up. I just had one stepper connected each x, y, and z axis. You can see all three are connected to the RAMPS board in the same order.
For my machine set up, I wired two steppers to the x and two steppers to the y. One stepper needs to run in reverse for each pair. Just reverse the connection of one stepper to make the stepper run the reverse direction.
If you have your steppers mounted, I suggest removing the belts, and test them all. reverse connections until they run the correct directions.
Hope this helps.