Let me give a short explanation. A 64-bit Wine needs to work together with 32-bit Wine because a lot of 64-bit apps for instance ship with 32-bit installers. The way we handle mixing 32-bit/64-bit is done the same way as in Windows. For files this means that all 64-bit stuff is in places like c:\Program Files and c:\windows\system32 (yes, system32 for 64-bit). 32-bit stuff is in c:\Program Files(x86) and c:\windows\syswow64 (yes, this is where 32-bit stuff is). A 32-bit windows program isn't aware that it is stored in the x86 Program Files, since that is handled under the hood (wineserver is taking care of it). Similar magic is performed inside the registry, so you have 'normal' and also wow64 keys for 32-bit stuff. A 32-bit/64-bit Wine requires duplicates of all wine libraries and binaries (except for wineserver which is shared and is a 64-bit app). Another warning if you are currently using a 32-bit Wine and you want to move to the 64-bit version, your old wine prefix won't work (remember, it lacks the wow64 magic). This is a transition problem.
