The first son was named after the father's father.
The second son was named after the mother's father.
The third son was named after the father.
The fourth son was named after the fathers eldest brother.
The first daughter was named after the mother's mother.
The second daughter was named after the father's mother.
The third daughter was named after the mother.
The fourth daughter was named after the mothers eldest sister, always.

 ALSO:
The 2nd wife's oldest daughter named after the first wife, using her full  name.
Children after those listed above were usually named after a favorite
relative with some possible exceptions:
   * If a child died in infancy, a later child might be given the same name.
        *When a newly ordained minister baptized his first child, if that child  were
            a boy, he would be named for the minister, if a girl, she would receive
         his surname as her middle name.
  *If a child were fostered, usually because of being orphaned, he may
      be named for the foster parent.
 

If you are sure that you have the earliest birth or baptisms and that  they are in the correct
order then, if John's first son is named Charles and his second daughter is named Elizabeth then
John's parents must be Charles and Elizabeth.  You get the picture. Of course this was not always true.
Though it was popular with most families. So if you have run into a dead end, this may be of help.
This information is courtesy of Paula Vaughn.