Some other good things to read up on
Poor Performing SQL Part 1 - http://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-1/
Poor Performing SQL Part 2 - http://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-2/
Stairway to SQL Server Indexes - http://www.sqlservercentral.com/stairway/72399/
Gail's articles - http://www.sqlservercentral.com/Authors/Articles/Gail_Shaw/148127/ - Especially the introduction to indexes articles