When creating the machine file it is important that the start and end points for each part are correctly aligned. The parts must be carefully designed so the start and end points of each color match up correctly or the design registration will not be correct. The first stitch in a row of an arrangement should start at the XY location of the last stitch of the previous row.
Note: If you want to mirror Part B, the start point should be at the top-center and the end point should be at the bottom-center.