During the logging phase (for any result) you'll be able to fully customize/modify your workout, which you can use to accurately represent any scaling or subbing you did.
Once you've selected your workout and you've begun logging your result, you can modify each portion of the workout so that it accurately represents what you did.
To swap out or change a specific aspect of a movement, click on the "pencil" icon next to the movement. This will bring up a screen that will allow you to edit specific aspects of the movement, or even swap out the movement altogether. Toggle new characteristics on in order to update their fields.
Click on the "Update" button to save your results. Continue the same process for the other movements, or move on to entering your score and adding notes.
Start by going through the process of logging a result for a given workout. See Logging a result: the Whiteboard calendar and Logging a result: not on your Whiteboard calendar for details on how to log results.
From the log page you'll be able to modify each aspect of the workout, starting with the structure of the rounds and reps. Click on the default rep scheme to change it.
Next, modify the movements as needed. Click on any of the movements. From the overlay box that appears, change, add, or remove attributes. Click on the name of the movement in the overlay box to substitute a completely different movement.
Finally, be sure to click the "Modified" button so as not to skew the Rx'd results. You'll also notice that as you adjust the workout above, the description below automatically gets updated with your version of the workout. In the example below, I've substituted pull-ups for ring rows and I've made the Thrusters 35# instead of 65#. The description reflects that.
**The notes section is also a good place to cite exactly how you scaled the workout, so feel free to write as much as you need to know for the next time.