My U3 drive contains tools that I either found on SourceForge or wrote myself installed on it. Yes, I said installed; U3 software isn't something you write or get from SourceForge -- it's something that you download from U3 Software Central.
In Visual Studio, icons can be added by right-clicking on the project and selecting Properties. You'll get a screen like the one in this scren; from there, you can hunt around for an icon that you've created, found on your computer, or downloaded from a Web site like Icon Archive.
U3 Package Prototyper does have several issues, the least of which is that it appends every program name with U3 Prototype of. I could live with this annoyance, but what I can't live with is the limitation of only a single executable. So, if I'm creating anything more than a quick and dirty U3 package, I use PackageFactory for U3.