The most painless place to pay is the nearest Recaudora (State tax office). It will take a matter of minutes unless the date you go coincides with the last days of January through April when long lines of customers show up to pay annual auto registration fees.
The Chapala office is located at Degollado 306, telephone 765-2064, hours 8:30-2:30 Monday through Friday. Be sure to keep the official receipt in your vehicle documentation files.