No relationship to the Navy. In 1864 every Confederate infantry regiment was expected to have an Ensign.

This is a FAQ on this and other boards. Here is one of many responses -
http://history-sites.com/cgi-bin/bbs53x/alcwmb5/webbbs_config.pl?read=35574

For discussions over the past couple of years, click on Search in the tools for this message board. Then use the search word 'Ensign'.