Our installer is written with Inno Setup and we are actually quite happy with it. Yet some customers keep asking for an MSI installer which they could more easily distribute
It makes no sense mixing install technologies.
If you are mixing you getting the first problem with the uninstall stuff. without changes you get 2 uninstallers of your program.
there are some articles starting with windows installer in the "entwickler magazine"
http://entwickler-magazin.de/
windows installer should be the only technology for your installations. its future proof and its stable!