I just have an Auto category in Quicken with the following subcategories (from memory, might miss one): Fuel, Depreciation, Insurance, Other (license plates, vehicle registration, smog check), Repairs, Maintenance (oil changes, batteries, tires).
I've minimized my Auto category as much as I really ever could. I flirt with the biking to work thing, but haven't yet for all the typical reasons excuses. I think my actual costs over the past few years have been lower than the IRS number by a fair bit because I have an old, fuel-efficient, good quality, non-depreciating car (95 Toyota Corolla).
I'll use the IRS rate on my taxes for charity miles, and sometimes I'll use that as the fully loaded vehicle cost if I'm considering driving vs. flying, although that doesn't usually make the final decision on how I travel.
2Cor521