I used keyclone under Linux for the last year or 2 doing a simple dualbox. At that time the window layout worked fine, although I had to play with it a while to get it to work properly.

More recently I tried keyclone after doing a fresh install of Xubuntu and was unable to get the window layouts to function properly. I would get multiple windows of the same size that could be moved around, but they did not reposition themselves at all.

Lax recommended that I give ISBoxer/Innerspace a try.

Innerspace works fine under wine. The ISBoxer configuration program will mostly work under wine if you install dotnet2.0 via winetricks. ISBoxer config do not display correctly. You can check and uncheck them, just you can not see them or if they are checked or not. Originally, I used Windows in a VM to run ISBoxer and export the config, which I then copied over.

Innerspace works well under wine. I am currently 5-boxxing and ran into an issue where instances of WoW were crashing, and realized I hit the 4GB memory limit of wine. Turning down the video effects settings helped resolve this issue. Currently, working fine in Outlands, still need to see about Northrend.