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 ...
- debuged and cracked.
- cloned by relatively untalented programmers looking to make a buck.
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; Eazfuscator.NET
for .NET apps or ProGuard
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.
Is there going to be issues with using this tool and wyBuild updating my application?
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.