I have not checked VS 2012 in this area, but I think it's the same as for previous version.
All that menu and command stuff is localized in a file called [mypackage].vsct which is the Visual Studio Command Table. The schema is described here: VSCT XML Schema Reference. When you used the wizard it probably created one for you.
As you can see in the schema, a Command is always linked somehow to a Menu (Commands Element), but there are a number of flags you can use to tweak this: Command Flag Element. Depending on what you do, I'd try the CommandWellOnly, DefaultInvisible and DynamicVisibility.
Anyway, if you don't want your menu to appear on the top menu bar, just can also just change the <Parent>
element of the root <Menu>
element in the vsct file.