Like some others here, I avoid packaged deals, so hardly an informed opinion here. I suppose the easiest thing is to leave the customary tip (I suppose 15% rounded up) and then there is nothing to deal with.
Then again, if you want to explore the issue and make a statement, I see nothing wrong with doing what you did ($6). In that case though I see no reason to avoid eyecontact with the waitstaff. If you choose to make an issue out of the charges and tipping, you might as well stand by your decision.
On a different note, does anyone have fresh opinions to offer on the New Jersey gas stations tipping custom? I am still confused about what to do there...