what method of commuting works best to get from Marin County to downtown San Francisco?
There are many ways to get from Marin County to downtown San Francisco.  You can drive a car, which can be fast in the morning, taking, say, 45 minutes or less if you leave before 8am.  Driving home, however, can take up to an hour and a half or more depending on traffic.

You can take a bus, which generally takes about an hour and fifteen minutes either way.  You can also take a bicycle to a bus stop, and the bus will carry your bike, but the spaces for bikes can fill up before you get on the bus, so check the route before trying this method.

Ferries that take you from Larkspur to the Ferry Building are also very popular.  You can drive to the ferry landing, park your car, and get on the ferry to downtown San Francisco.  When the weather is nice, this can be a wonderful way to either unwind or catch up on work.  Ferries can be subject to weather delays and cancellations, so check the weather before trying this method.

Finally, you can take a bicycle or even run all the way in to downtown San Francisco from Marin County.  Bicycling is generally an hour to hour and a half round trip, but again check the weather and your fitness level before committing to this.  And most of all, make sure you eat enough calories during the day to fuel that ride home!  There are some intrepid souls who have taken to the water and swam from Cavallo Point to Aquatic Park, which takes a lot of practice and planning.

There are many ways to commute to San Francisco from Marin, so feel free to mix and match and try new methods to keep yourself happy, fit, and motivated for that awesome job in the city!