Check Templates: Company has 2 subsidiaries with 2 different paper check formats. I can create different Advanced PDF Check Templates but how do you select which one is printed other than switching the preferred form?

Use a freemarker #IF looking at subsidiary. I'm assuming the only differences are going to be in the body so you can have the statement in there and just include both in one pdf. If not, use a

pdfset

and define both templates in full.