If your residency application has been accepted by Migracion in SD, then your residency application is ostensibly approved and you are en processo. Keep a photocopy of your application certificate of deposit, your main passport page and the copy of the residency visa page and you shouldn't have any problems while your file sits on someone's desk for months.
If you don't have a copy of your certificate of deposit, get one. This is your "I'm legally allowed to be here so stick it" document.
More and more, gringos stopped at any manner of check point will first be asked for their passport or cedula, then their driver's license if in a car. Status is checked first, then the real reason for the stop. At this time, the emphasis is on immigration status and illegal firearm possession and then any vehicle related infractions/tax omissions/paperwork issues.