I discovered you can have multiple ways to add apps into the secure folder. For most of my apps I installed from the regular side and then added it to the Secure folder.
If you only want the app to appear in the secure folder, you can uninstall it from the regular side. However, I noticed that if you do this, those apps don't auto-update. To update them, you have to manually install it again, then uninstall it.
[SUB]I just verified this -- I found one app that I had exclusively in Secure Apps but it was an older version. I installed it again, then immediately uninstalled it.[/SUB]