The bottom edge of the water bottle is located with respect to the lower water bottle boss. This measurement is taken parallel to the tube (shown here as 15mm). The side of the water bottle is located by an offset distance from the edge of the tube (shown here as 14mm).
The water bottle bosses are located by a distance from the bottom bracket. BikeCAD Pro calculates the location of the water bottle boss from the end of the tube. This is illustrated below.
For more on adding water bottles, see here.