As you have discovered inconsistency in spelling of place names (and surnames) is well known to those who have conducted research into their Irish family history. Place names, originally in Gaelic, were anglicised from the 17th century, by settlers with little knowledge of the Irish language. This resulted in many different spellings of the same place name. An ‘official’ and standardised spelling of townland names for all Ireland was established, by 1842, by the Ordnance Survey and published in the Townland Index and on Ordnance Survey maps.
As Martin confirms no Irish place name of Runiskillen is recorded in the Townland Index. This, of course, doesn’t mean that it doesn’t exist; it could be a corruption/misspelling of a place name.
Although a search of the Placenames Database of Ireland at https://www.logainm.ie
reveals no Runiskillen it makes 2 possible suggestions the town of Enniskillen in County Fermanagh and the townland of Rinakilleen in County Mayo.
If you suspect that your ancestors were from the province of Ulster and in particular from County Fermanagh it would seem reasonable to assume that Runiskillen refers to Enniskillen. Enniskillen played a significant role in the Williamite War in Ireland, 1689 to 1691, when locally raised regiments operating out of Enniskillen attacked Jacobite forces throughout Connacht and Ulster. Brief history of Enniskillen can be viewed at https://www.libraryireland.com/topog/E/Enniskillen-Tyrkennedy-Fermanagh.php