I also reinstalled it to see if it would work with it, but as soon as I did that, the apps disappeared out of the drawer. Upon uninstalling, they reappeared, so it doesn't look like Secure Folder will play nice with the Google Now Launcher.
Re: Secure Folder & Google Now launcher not playing well
So I uninstalled Secure Folder, and the apps finally showed up in the drawer. Sorta disappointing if I can't have both active.