Ireland, and in particular Ulster, was heavily settled by people from Scotland, England and Wales in the 1600s. Most of those were Protestants, though there were some RC settlers too. Those from England and Wales tended to be identifiable later because they were members of the Church of Ireland; those from Scotland were mostly Presbyterian. The settlement was known as the plantation of Ulster. Here?s a link that tells you a bit about the plantation of Ulster.
http://www.ulsternationalist.freeservers.com/custom2.html
The estimates vary but it is reckoned that in the 100 years to 1700, about 100,000 Scots settled in Ireland (representing about 10% of the entire population of Scotland at the time). Throughout the 1700s, about a half their descendants ie another 100,000 people left Ireland and went to the USA and what is now Canada.
So to answer your question about whether there were Protestants in Ulster in the 1700s, the answer is yes. In fact they formed the majority of the population.
Tracing relatives who emigrated in the 1700s is very difficult indeed. Very few churches have records that go back that far, and there are precious few other records form the period either.
Using this link, you will see that in the mid 1800s, the name McDowell was most commonly found in Cos Antrim & Down. That would be highly indicative of Scottish origins, as those 2 counties were the most heavily populated by Scots and because the name McDowell is Scottish. If your family was also Presbyterian (as I strongly suspect they were) then you have 3 strands of proof of Scottish origins. There are no records of where the Scots settlers came from (save for a few major landowners) and so finding out exactly where in Scotland they originated is not normally possible. In general the majority of Scots settlers came from the South West of Scotland and around Edinburgh and the Scottish borders. That?s about as far as you can usually say.
http://www.irishtimes.com/ancestor/surname/