As of wyBuild 2.6.16 you can handle this 1 of 2 ways. Either install the 32-bit & 64-bit files to everyone's machines.
Or have a separate wyBuild project for the 32-bit and 64-bit versions. That is, the 32-bit project will have every file that consists of your 32-bit version of your app, and the 64-bit project will have every files that consist of the 64-bit version of your app.
Does that make sense?