This is a link to a good tuning guide over on CF. There is a downloadable version of it as well, and an example tune that can be downloaded.
http://www.cumminsforum.com/forum/3rd-gen-performance-parts-discussion/1102386-tuning-basics-guide.html
http://www.cumminsforum.com/forum/3rd-gen-performance-parts-discussion/1102386-tuning-basics-guide.html