If you click the Eve shortcut to start a second Eve client it will over lay over the other client. To resolve this and run two clients in two seperate windows you can do the following.
Create a shortcut with the following command for your first client. (I call mine Eve (Client 1))
/opt/cxgames/bin/wine --bottle EVE -- explorer /desktop=0,1440x900 "C:\Program Files\CCP\EVE\eve.exe"
Then you create a second shortcut (link to application) using the following command. (I call mine Eve (Client 2))
/opt/cxgames/bin/wine --bottle EVE -- explorer /desktop=1,1440x900 "C:\Program Files\CCP\EVE\eve.exe"
you need to change /opt/cxgames/bin/wine if you did a single user install or if you installed to another location to point to your correct install location.
These commands will start Eve in a 1440x900 window, you can edit the resolution setting to what ever size window you want, however you may need to manually set the same size in the Eve graphics options or when the game starts the window will re-size to the dimensions specified in the Eve graphics config
NOTE: While this is still valid a Window can also be set by using the graphics options in the Eve client.