It is worth noting that the technique of using a reference star near in elevation to the target is technique developed to make it easier for amateurs. Because professionals have stable setups and know their atmospheric conditions, they tend to use a standard instrument response measured infrequently using precisely measured spectrophotometric standard stars, combined with a measure of extinction on the night together with an atmospheric model. ISIS does have the tools to do this though.
http://www.astrosurf.com/buil/isis/guide_response/method.htm