1. First, if there is a known direction of acceleration, choose one axis to be along the direction of acceleration.
2. In statics cases choose a direction for the axes so that as many vectors as possible line up with either the x- or y-axis. For example, in the figure below a choice of an axis that is tilted with respect to the horizontal results in two vectors lining up with the axes, while the standard horizontal and vertical alignment results in only one vector lining up. The tilted axis could be a better choice in this case.
Andes can only give help if you choose an axis that is a good choice for the problem you are working on.
NOTE: In the current version of Andes the x axis can only be oriented between 0 and 90 degrees in a CCW direction with respect to the right pointing horizontal. However, this restriction will still allow the rules above to be followed, although one might have to rotate the system to point a negative x or y axis in a specified direction.