I've been entering what I've gathered (as time allows) regarding this Atkinson family in a tree on

www.myrootsplace.com.

If you go there and do not see the search box immediately, click on the 'genealogy' tab and it will take you to search.

This tree is entered very cautiously, with as much documentation as has been found. There are NJ Atkinsons in this tree, who are not connected.

The John Atkinson you found for 1880, with wife Francis and his mom Margaret, does indeed look like the son of John, brother of your ancestor Thomas, and John's wife Margaret (Glover).

Good hunting!