When using Sputnik Tool's main tube mitering fixture for mitering the top tube or the down tube, you would start by mitering the front end of the tube.
To miter the back end of the tube, you would fit the Sputnik Tool mitering fixture with a phase block which matches the diameter of your head tube. This phase block keeps the tube perfectly aligned when mitering the back end of the tube. You can show this phase block in BikeCAD Pro by selecting the phase block icon, clicking on the eyeball icon and choosing the phase block specs that match your head tube diameter. While you could use BikeCAD's miter to miter length dimensions to line up the edge of your rear miter, the Sputnik Tool mitering fixture features a scale which gives the distance from the center of the rear miter to the pivot point on the phase block. It is much simpler to setup the mitering fixture based on this dimension rather than the miter to miter dimension. BikeCAD Pro also provides this dimension. You'll find it under Mitering >> Phase blocks >> Top tube >> Center to center.
The display of the phase block in BikeCAD is only there to help visualize the mitering process. Don't forget to turn off the display of the phase block once this task is complete.