wyBuild automatically detects which exe's are .NET executables at build time (when it builds the update). You don't need to do anything special. Just add the files to wyBuild.
The only time a .NET exe isn't ngen'd is if it's a .NET 1.0 or 1.1 exe. This is because NGENing has so little effect on .NET 1.0 and .NET 1.1 exes that the speed improvement is negligible (and in some cases causes speed loss).
But .NET 2.0+ exe's will always be NGEN'd. Are your exe's .NET 2.0 (or 3.0, 3.5, or 4.0) exe's? If this is the case would you mind sending me one of your exe's to support@wyday.com?