I think it’s most likely that the Andrew who died in Cross in 1886 is your family. His wife looks to have been Charlotte. Here’s her death:
https://civilrecords.irishgenealogy.ie/churchrecords/images/deaths_returns/deaths_1893/06014/4711906.pdf
There was still a Rooney family in Cross in 1901:
http://www.census.nationalarchives.ie/pages/1901/Down/Tofanny/Cross/1233949/
And 1911:
http://www.census.nationalarchives.ie/pages/1911/Down/Fofanny/Cross/242926/
Mother was Mary Magill. Can’t find a marriage but I’d guess William was Andrew’s son.
Probate abstract:
Rooney William of Cross Bryansford county Down farmer died 6 December 1947 at Down Mental Hospital Downpatrick county Down Administration Belfast 20 February to Edward Rooney farmer. Effects £103 15s
Newry Reporter of 31st July 1906 reports the sad drowning of Robert & Joseph Rooney of Cross. They had gone for a swim in the River Phimla at Moyad but were not swimmers and had got out of their depth in a whirlpool and drowned. Their bodies were recovered. An inquest was held.
https://civilrecords.irishgenealogy.ie/churchrecords/images/deaths_returns/deaths_1906/05556/4559483.pdf
Joseph born 30.9.1884 & Robert 18.1.1887.
Kilcoo Church of Ireland’s baptism records start in 1786. You may get Charlotte’s maiden name from the childrens baptisms. Copy held in PRONI. Rootsireland also has some coverage (subscription). I don’t see a marriage for Andrew & Charlotte in the statutory records so that suggests they married pre April 1845. I suspect it was pre 1840 as what looks to be a son John married in 1860 when he was aged 40. Ages on death certificates in the 1800s are often just guesses, so I suspect Charlotte was born earlier than her age on her death cert suggests.
This might be another of Andrew’s sons:
https://civilrecords.irishgenealogy.ie/churchrecords/images/marriage_returns/marriages_1860/09591/5478023.pdf
Possibly a daughter:
https://civilrecords.irishgenealogy.ie/churchrecords/images/marriage_returns/marriages_1871/11329/8158314.pdf
There’s a tree on Ancestry with the above family (Jacquie Whetham tree). After their marriage, the above couple seem to have moved first to England then to Scotland.