If wisdom teeth are causing you pain, you might need to have them pulled. A lot of people get rid of their wisdom teeth since they are not really needed and can cause severe problems. An infected or impacted wisdom tooth will need to be removed immediately, but it is best to extract it before this happens.
When flossing, gently slide the floss up and down the sides of BOTH teeth. Also, slip it beneath the gums and slide it back and forth to clear out any gunk. There are also brushes you can use which slip between the teeth and clear out anything left behind if floss doesn't do a good enough job.