1. Install wine and timidity. I presume xephyr server is installed.
2. Insert CD and run setup.exe with wine. Install game to default location, install QuickTime when it asks.
3. In one terminal window run timidity midi server (if you want background music): `$ timidity -iA -B128,8 -Os`
4. In another terminal window start the game like this: `$ Xephyr :1 -ac -screen 640x480x16 & DISPLAY=:1 wine "C:\\Program Files\\Segasoft\\Obsidian\\Obsidian.exe"`
In case you don't have physical optical drive you can use CDEmu to mount disk images, but it has to be installed from additional repository and has a bit of complicated setup.
I have been playing a bunch of old Mac games on SheepShaver. Sometimes they just work better than the Windows versions under Wine.
I've not. When I get back to it, that'll be on the list of things to try.