Well I have the same setup here and this is the way I have my setup:
My Full job runs on Mondays at 11:00pm and I selected : FullBackup reset archive bit for method in the Job preferences.
My Diff job runs Tues-Sun at 11:00pm and I selected Differential Changed Files for method in the Job preferences
My Diff jobs will grow as files get changed throught the week which is ok and the more the files get changed the bigger the DIff's, so I guess in theory your final diff can get as big as your Full.
If you make a copy of another job and you make changes to the copy, you will also modify the original job. Make two independent jobs one for your Full and another for the Diff.