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.
PackageFactory for U3 also has an Advanced Mode where it’s possible to add company name, version number, description, an application URL, and more executables.