Yes.. you must include the main folder and then exclude sub-folders..
Why? A backup of Applications will happen once.. the first time it is included.. after that only changes are backed up and should be.. upgrades to Apple apps and should really be part of your backup.
And the MAMP application (no idea what it is) is behaving poorly to not use your Documents folder.. as a rule no Application should store current work in Applications. One would have thought after years and years of MS doing such things and finally getting it sorted out, we would never see it on a Mac.
See if you can force a change in the default folder.
If not you might be able to create a symbolic link to folder in the correct area. This is outside my experience.. but see
http://apple.stackexchange.com/questions/115646/how-can-i-create-a-symbolic-link -in-terminal