The direction that the skids and base lumber run are some of the most fundamental basis of a styles construction. International standards are written specifying orientation as part of good construction. As a user you may change the orientation as desired but there will need to be additional manual adjustments.
Skids - You can change the direction of the skids by changing the code from LOD to WOD or visa versa depending on the style family. LOD calculates the 'length of the outside dimension' and WOD calculated the 'width of the outside dimension'. However, light duty crates, by standards, run the skids width-wise (F-A), medium and heavy duty run the skids lengthwise or (Left to Right). Lumber base boards will always run opposite the skid direction. As a suggestion, before reversing the direction of the skids and base lumber, look at a different style group that already applies the materials in the desired direction and adjust to using heavier or lighter materials.
Base - The orientation of the base is one of the most fundamental basis of the style. If you manually enter a value designed to change the direction of the base lumber, Crate Pro does not calculate the boards as being rotated to the new direction and give you an updated quantity with a new rip or spacing value. Crate Pro continues to see the boards running in the direction that the style dictates and will simply adjust the length of the board to meet your new value. You will have to manually determine the values you need.