As a former car salesman, I have experienced many deals where the customer was 'upside down' (owed lots more than the car is worth).
Taxes, extended warranty, undercoat, and many other business office add-ons at the dealership will seriously overload the loan value of that car purchase.
It is no big deal to roll all that outstanding debt into the new car loan, but it really makes the problem worse-your $16 500 Mazda 5 could easily have more than $20 000 borrowed against it. Subtract the 30% depreciation that new cars experience when registered by the new owner, and one week into ownership, you are upside down by $10 000.
In you case, R1FIGHTER, if I understand your situation correctly, you owe $6500 on your Jetta and are offered a $3500 trade allowance by the dealer. Is that right?
If you accept the deal as offered, this will require you to finance an extra $3000+.
I assume that the dealer has deducted from the Jetta's value the cost of those 'major repairs'? If this is correct, consider finding a loan for the longest term possible (60-72 months) and include an extended warranty with a massive mileage allowance.
Sounds like your best option is to forget to remove the keys while parked in a dark side street.