If you're installing using apt then aren't you fetching the package from Ubuntu's repository?
In that case it's the Ubuntu maintainer's problem, not the upstream project's.
Any details about how to install menu entries or add an icon to a menu entry (i.e. a .desktop file) is entirely dependant on the desktop environment, whatever it is. Sorry.
Having said which, my general experience is that most desktop environments (with the notable exception of KDE) have minimal ability to edit .desktop files. There are usually various XDG utilities, but I can't remember whether one of those has the ability to edit an existing .desktop file rather than create one from scratch.
MarkMLl