There are two Windows applications that I use regularly via Wine. One is Winbox from Mikrotik and works great. The other is a phone/chat application which is buggier than a hive of bees. Anyhow, they seem to conflict with each other, which is a problem. Luckily Wine provides a solution: WINEPREFIX.

1. From a blank Wine configuration, install the first application. This will create a default Wine configuration.
2. Move the default Wine config to a new directory, e.g. mv ~/.wine ~/.wine-app1.
3. Repeat install and move for the second application, e.g. mv ~/.wine ~/.wine-app2

Now when you want to run App1, simply point wine to its custom config: WINEPREFIX="${HOME}/.wine-app1" wine App1.exe. Same goes for App2 and on, as many apps as you want to install. Very simple.