Well, obfuscation is useless. The 2 things it's supposed to prevent (crackability & reverse engineering the behavior of your app) it can never prevent. Namely, if the app still runs, and behaves as you designed it to behave, then it can be ...
[*:2n6ba1e3]debuged and cracked.[/*:m:2n6ba1e3]
[*:2n6ba1e3]cloned by relatively untalented programmers looking to make a buck.[/*:m:2n6ba1e3][/list:o:2n6ba1e3]
You can litigate number  (with or without obfuscation). You can never prevent number . Thus, obfuscation is pointless.
If you're going to use obfuscation you might as well use a free one; [url=http://www.foss.kharkov.ua/g1/projects/eazfuscator/dotnet/Default.aspx:2n6ba1e3]Eazfuscator.NET[/url:2n6ba1e3] for .NET apps or [url=http://proguard.sourceforge.net/:2n6ba1e3]ProGuard[/url:2n6ba1e3] for Java apps. They're just as useless as their commercial counterparts, except you don't have to waste money on something of no value.
[quote:2n6ba1e3]Is there going to be issues with using this tool and wyBuild updating my application?[/quote:2n6ba1e3]
No, there won't be any issues. However there are some side-effects of using obfuscators that introduce "encryption" into the obfuscation process. Namely, your patches built in wyBuild won't be as small.