Also here is another link though will post the section here to save people time trying to find it.
Depth of transplanting has normally been to the top of the roots or root ball. Research from Florida with the variety Jupiter suggests that pepper transplants may benefit from being set deeper, up to the first true leaf. Thirty days after transplanting, plants planted to the first true leaf had more leaves, greater plant dry weight, more blooms and less lodging than transplants planted to the cotyledons or to the top of the root ball. Other data from Pennsylvania suggest caution however. Soil temperature and moisture would be important considerations.
http://groups.hort.oregonstate.edu/content/peppers-0