The mother of Charles H. Allen was Henrietta Pond whose mother was Hannah Wentworth. The Wentworth family is detailed in the Wentworth Genealogy:English and American by John Wentworth, LL.D.; Chicago, Illinois: Little, Brown and Company, 1878, Vol 2.The author says that Hannah had a previous husband named Charles Clapp.This might explain the Charles portion of Charles Allen's name.And, it is possible that her second husband Charles Franklin Allen adopted both the child Charles and his sister Francis.We have not located primary documents to prove this information, however. Nineteenth century genealogists didn't seem to think it necessary to include their sources!
Charles Franklin Allen originated in Salem, Mass.His father was Capt. Charles Henry Allen whose life is written about in George Granville Putnam's Salem Vessels and Their Voyages; Salem, Massachusetts:The Essex Institute, 1925.
An Allen genealogy that you might want to look for is: Genealogy of the Allen Family of Manchester, Massachusetts from the Earliest Settlement to the Year 1886 by John Price; Salem, Massachusetts: Salem Press, 1888.