Adobe Lightroom Workflow Basics - Applying Filters, Flags and Ratings
The title pretty much says it all. Adam talks about his workflow and how he applies filters, flats and ratings.
Keep in mind that over time you will find what works the best for your own personal work flow. This is just a basic guide for what Adam does and I personally do some things slightly different when it comes to flagging and filtering. But again there is no right or wrong way to do this and what works for you is what you should stick with.