There is no "Flash for Windows", but I presume you mean "Flash for Other Browsers" (aka NPAPI, or PPAPI for Chrome), or perhaps you mean a standalone Flash player?
But you shoulnd't need to uninstall anything manually. Just download the Flash for Internet Explorer (aka ActiveX) and install it. It will overwrite/remove any old versions of the ActiveX Flash Player, and shouldn't touch the other versions.
Moved to the Installing Flash Player forum.
You can have both the NPAPI Plug-In (Firefox, Opera, etc) and the ActiveX control installed simultaneously. Chrome also has it's own version of PPAPI Flash Player.
The uninstaller will remove both the NPAPI and ActiveX controls. You only need to run the uninstaller if you want to downgrade to an old version of Flash Player (which is generally not advisable for security reasons) or if you want to remove Flash Player entirely. The browsers will also let you disable the Flash Player plug-in using their plug-in management settings, so if you wanted NPAPI Flash Player in one browser but not another, you could disable it in the individual browsers without actually deleting the software. If you want to upgrade or just install Flash Player for a different browser, you only need to run the appropriate installer.