There may be a misunderstanding of what you are able to do.
You can only create profiles for applications. One profile for each application. You can not have multiple profiles per application (without some hacking on your part).
When you create a profile, you specify the name of the application's executable. When the driver notices this application in focus, it switches to your profile. If the application never gets focus, say it doesn't have a window, the driver will never know that it is supposed to use your profile.
You don't have to have the application running to create a profile for it, though it is easier since you can use the GUI to select the application executable. If it isn't running, you have to find the correct executable name. If the application doesn't have a window, that is a good indication that we won't be able to detect it. There are occasionally some permissions issues that prevents us from detecting an application. Running as admin may help those issues.
There are ways of hacking around this design, but I'd have to specifically work with you to let you know what you can and can not do.
In particular, you probably have noticed that there is a special "desktop" profile. This is used if there isn't a recognized application in focus. I think we now call that the "Default Profile" in the GUI. This profile can be made to do desktop-type things, such as moving the cursor around, mouseWheeel, etc. The buttons can be mapped to 2D mouse buttons. You can modify this profile to your heart's content, but there is only one of them.
We are assuming that you will mouse around to start, or switch to, an application. Then you will have a profile for that application.
Does all that make sense so far?
If this doesn't match with the way you were assuming the driver worked, it may be best to delete all your saved profiles (save them somewhere) and start over.