In your specific case, neither 'was' nor 'were' is best; you should say "if it is running". "If it were running" is subjunctive case, used to describe hypothetical situations: "If it were running, I would stop it first, but it's already stopped." More @Wikipedia
Hover over any link to get a description of the article. Please note that search keywords are sometimes hidden within the full article and don't appear in the description or title.