Traditionally the principal way of tracing families prior to statutory registration is church records. You say that your Ballyholland Fitzpatrick family used Clonallon church. The records for that church start in 1826. Hilltown is in Clonduff parish. Their records start in 1850. So it’s going to be difficult to connect families in Ballyholland and Hilltown prior to those dates.
Unless someone knows of a connection or you get a DNA match, I can’t think of an easy way of finding family links. As a general comment Fitzpatrick is a very common surname in Ireland – there are over 10,000 in the 1901 census - with 749 in Co. Down. They aren’t all going to be related.