While I've never found any documentation discussing this my personal experiences have shown that Wine assigns different letters to each prefix, which I guess makes sense because when you install multiple versions of Windows for real there are certain circumstances that can result in each installation having a different letter drive rather than all using C:\ (Eg: the use of logical partitions.) but it's still really weird.
Short hand commands for Wine only seem to work for default prefix because the command assumes the use of C:\ . When you install wine it creates a prefix and assigns it as C:\ any additional prefixes you make may have different letter drives. You will need to find out which letter drive your 2nd prefix is using. Most likely D:\ .
One way to be sure would be to copy cmd.exe from Windows (Not the Wine cmd.exe it doesn't work) to the prefix and launch it. It's located at C:\Windows\System32\cmd.exe and it will read something like D:\Users\Username.
Example Wine Command For Launching 7-zip:
wine start 'C:\Program Files\7-zip\7zFM.exe'
Keep in mind that if the software installed within the Wine prefix is configured for a C:\ setup but is running from a D:\ configured prefix, then it won't run unless it's a simple program that doesn't need to look for other files or that uses %SYSTEMDRIVE% or a variant when searching rather than D:\ . Wine really needs to provide a more in depth explanation of the multi-prefix feature, because clearly some odd stuff goes on.
