Another old thread in FAQ, a year, or so so let's update it and nail this issue down. Here's my take.
A drawing, whether on paper or in a CAD program, usually have the axis set up as we learned in grade school, e.g. upper right quadrant are positive values. Thus, in effect, our pencil is the quill moving over the table.
However, the mill is moving the table beneath the quill, e.g. it is NOT moving the quil itself. Hence, moving the table to the far right and away from you finds the origin, or 0,0 of your drawing. Thus, the table moves to the left for +X (in effect the quill moving to the right) and toward you, for a +Y value (in effect moving the quil up the Y-axis).
Confused yet?
Machine center (X,Y) on a FADAL mill is usually center of travel of the table however, when milling a job, it is convenioent to relocate this to be coincident with the 0,0 of the part itself. This is especially handy when you have multiple vices on the table because then you set up offsets from the first jaw for each subsequent vice, e.g. a job with four vices on the table with each set 6 inches apart means you incerment the X-value by the with of the vice plus 6 inches for each subsequent job.