You'll have to forgive me, as I've not used minimenu much, but changing a PND's icon is as simple as dropping a PNG file with the same filename (before the extension) as the PND, and according to the wiki at least, that ought to change the icon. As I don't use minimenu though, I don't know if it has an option to do this after install, or whether you'll need to boot into XFCE to do it, or move your card to another computer to do it. I believe minimenu will write .ovr files for you though, so it may have the option.
I'm a little mystified by your reference to PND manager though. As far as I've noted, PND manager doesn't let you override PND settings at install time.