Can I run applications directly off of a Windows installation without reinstalling them?
Generally, no. Unless you know otherwise, you should leave your Windows installation alone and install things “fresh” into Wine. Most applications store their configuration data outside of their own folders, such as in the Windows registry. This isn’t unique to Wine: you’ll run into a similar problem under Windows itself if you try and run applications from another Windows installation. Wine (or the other Windows installation) has no way of seeing this data unless it was written into Wine’s registry by the program installer. Some applications, however, are designed to be “portable” and don’t use the registry at all, instead storing all of their settings in a file alongside the executable.