Will there be a Flash Builder Update from 4.5 to 4.6 via "Help->Search for Flash Builder Updates" or do I have to re-install manually?
You can download the full installer from Adobe.com. Please note: you must uninstall your previous version of Flash Builder 4.5 or 4.5.1 before installing 4.6. By default the Flash Builder uninstall program will preserve your preferences and workspace so you can easily reimport them into Flash Builder 4.6. If you require the standalone Flex 4.6 SDK, you can download the build from the Adobe opensource site.