If your workout is pulled from Strava, it won't mark it as an FTP check, but it's easy to do: from the Rides tab on your Dashboard, find the one you want to edit and click the pen icon (edit). On the next screen there is a tick box which you check to mark the workout as an FTP check.
For rides where you didn't do your FTP check, just leave it alone. VeloPro will see that it wasn't your check and won't treat it that way. In fact, when you do an FTP check, you need to mark it as such when you upload it. There is an FTP Check box on the upload dialog for that.