You've chosen the custom option. Being able to choose exactly where the stays attach is meant to be one of the advantages of the custom option. In case you are not aware, the Sx, Sy, Sz, Cx, Cy and Cz fields are where you input the end points for the stays in X, Y and Z coordinates from the rear axle.

If you choose a dropout from a static drawing, BikeCAD will automatically set the end points of the stays to something that is reasonable. However, unless those dropouts are socket style dropouts, you should still feel free to adjust the location of the end points. With plate style dropouts, you'll typically slot the stays and insert the dropout into the slot, but that slot can be cut to various depths. Similarly, with hooded dropouts you can attach the stays at various points around the circumference of the hood. This is shown below: