Exactly, you cannot use the FOP2 Manager to configure the buttons themselves. There are many ways you can use to set the buttons by hand... you could leave the user configuration to be automatic/managed, but not the buttons themselves. One way to do that is to modify autobuttons.cfg and change it to
buttonfile=mybuttons.cfg
and then create a mybuttons.cfg with your agent buttons.
Now, for users, you won't be able to set groups (and you will have to be sure to not click on any group on the users tab in the manager).
There are many other ways to handle it, like having directly user=xxx lines in fop2.cfg and not use #exec at all, or write your own auto config scripts.
Best regards,