Why is my dimension negative?
When you add a dimension from a Line to a Point, the dimension itself can be Negative or Positive.
Why is this?
•  The Line from which you dimension the point has its own XY Coordinate System. 
•  The positive x–axis of the Line is from the startPoint to the endPoint' (the places where you mousebutton down and mousebutton up at each end of the Line) 
•  Therefore, when looking along the positive x–axis of the Line, a 
o  dimension to a Point that is to the positive Xaxis of the Part, is negative with respect to the yaxis of the Line. 
o  dimension to a Point that is to the negative Xaxis of the Part, is positive with respect to the yaxis of the Line. 
When you add a dimension from the X or Y–axis of a Part, the dimension itself can be Negative or Positive.
Why is this?
•  Each axis is treated as a Line. Thus, the axis itself has its own XY Coordinate System. 
•  The less obvious case is the Y–axis: 
The positive X–axis of the Y–axis(!) is from the Origin and in the positive Y–axis direction. Therefore, when looking along the positive X–axis of the Y–axis, a
o  dimension to a Point that is to left is negative. Therefore, a dimension to a Point in the +X–axis direction of the Part is negative. 
o  dimension to a Point that is to right is positive. Therefore, a dimension to a Point that is in the X–axis direction of the Part is positive. 
Why is the Dimension along the X–axis negative? Note: Xaxis, Yaxis : coordinatesystem of Part, xaxis, yaxis : coordinatesystem of element, and a Line. Dimension convention in MechDesigner: All Lines and Axes have a Coordinate System (Origin and +x,+y) . This includes the Partaxes : X–axis and the Y–axis. Each axis has an origin and a +x–axis direction and a +y–axis When we dimension using the Y–axis, or a Line in the Yaxis direction, then its +x–axis direction is along the +Y–axis of the Part. 

In the image, the area with the 'patch' is all –ve in the Coordinate System of the Y–axis, or Line in the Yaxis Therefore, is this case, when we dimension the Point along the X–axis of the Part, it is along the negative direction of the yaxis of the Line. 