Wine version: 1.2.2 (Current version)
Run installed Safari, executable for Flash player to install.
Configure Wine->Windows XP->Graphics->uncheck Allow Pixel Shader. (This fixes the Quicktime bug, which allows you to watch Apple's Quicktime movies.
To install Flash inside where you installed Safari:
Click Install->Install a .pol package or an unsupported application.
Manual Installation->Forward->Edit an existing application->choose the prefix you named where you installed Safari, then please select the install file to run, and choose the Flash Installer file which you downloaded, and install. After installation completes, in POL, click Cancel. This is how to install other applications inside a wineprefix you created.