If I accept a partial amount owed on back rent owed, after serving a 14 day notice of eviction, and our new agreement (no lease, just always been a 30 day tenant at will) is broken,can I re-start a 14 day notice again, but go through the complete process through the courts to actually evict the tenant?

Is the notice requirement only 14 days in Massachusetts? I didn't know that. It's 30 days in most places.

But no; if you gave due notice, partial payment shouldn't require you to give new notice, before you may sue to evict. In fact, unless it's a "pay or quit" notice you gave, even full payment wouldn't prevent you from proceeding to an eviction action. And I assume that (if it is indeed a "pay or quit") your notice required the tenant to pay the full amount due, plus late fees if applicable. Thus if they failed to pay the amount demanded, you should be able to proceed.

Please clarify: what is this "new agreement" to which you refer?