Part of the Harmony Remote FAQ:
9. Is there a way to reorder devices and/or activities?
For remotes that have physical buttons for activities, you are not able to reorder the activities listed under the "More Activities" option.
Logitech support states that the Harmony 600, 650 and 700 (and possibly other Harmony remote controls) do not have the native ability to 'Reorder Activities'. This means that if the remote chose to place your favourite 'Activity' on the 4th page, you would have to scroll there every time you wanted to access that 'Activity'. This ordering feature is missing on the recent versions of the desktop software (7.7.0), despite the fact that previous versions of the software supported this. This workaround functions by accessing an older web version of the software (7.3.0) which is still works on newer remotes, although not in the most user intuitive way.
Reordering Activities Hack For Harmony 650
Step 1) Login to the following website: http://members.harmonyremote.com/. If you have been using your Harmony desktop software, this will have all of your settings stored here.