How to add a citation to a sentence that has parentheses at the end?
This depends on the writing and citation style you are using. In APA you should use a semicolon to separate the citation from the acronym:

However, methane has a higher Global Warming Potential (GWP; IPCC, 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors; IPCC, 2013).

Source: http://blog.apastyle.org/apastyle/2013/05/punctuation-junction-parentheses-and-brackets.html