Lauren, there were several Samuel Allens. There was the Samuel Allen of Barnstable,MASS the town formed when Plymouth became crowded....
There is my Samuel who came from England, born 1588 from Braintree,Essex, England, and settled in Braintree,MASS, moved to CT with a group and settled in Middletown,CT
There was another Samuel, I believe of Roxbury or someplace else - he is not my line.
I have Samuel and Samuel - but not proved who my Samuel's father is - could be George, or another person....there is controversy over this...Samuel being such a common Biblical name.
You might try looking at the Samuel of Barnstable - who married there and whose children lived there until moving on to CT.
We know that there were some Joseph's in the famous Ethan Allen line - so perhaps your Joseph is of that line - Ethan was distant cousin of my Samuel - as they lived in CT and then eventually ended up in VT - but not in the same places.
Hope this helps - You can look up Ethan Allen's lineage on-line - and go to MASS and counties there for lineages of the other Samuels -