Unless I am mistaken, there is only one: Nick Saban, who won the BCS Championship at LSU (2004) and at Alabama (2009).
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GA Southern
Division 1 (BCS) Notre Dame 8 championships Division 1 AA (FCS) Georgia Southern 6 championships Division II North Dakota State 5 championships Division III Mount Union 10 championships
The University of Michigan has the most with 11 national championships the last in 1997. GO BLUE
The Bulldogs have won two consensus NCAA Division 1-A college football National Championships and 12 Southeastern Conference championships.
No Alabama football coaches have won national championships.
UConn has been playing division 1A football since 2000. Between 1978-1999 they were a 1AA team, between 1973-1977 they were a division II team, and between 1937-1972 they were a College Division team. During their existance, UConn has not won a national championship in football. They are credited with 15 conference championships, all in the Atlantic 10 between 1949-1989.
The University of North Carolina does not have any national championships in football.
According to the College Football Data Warehouse: For the 2011 football season, the following teams won National Championships: Alabama - Division I-A North Dakota State - Division I-AA Pittsburg State (KS) - Division II Wisconsin-Whitewater - Division III
Florida and Alabama
The University of Michigan has 11 National Championships. The University of Miami has 5 National Championships.
The university claims 8 national championships.