If you middle-click a floating contact, they will temporarly dissapear (8secs by default) so you can click on the window underneath.
To set the global options for the floating contact windows you can go to:
Plus! > Preferences > Messenger > Contacts on Desktop
Individual options for each floating contact window can be further tweaked by right-clicking the floating contact > Display Settings.
Then there are two registry tweaks which you can set in:
HKEY_CURRENT_USER\Software\Patchou\Messenger Plus! Live\<your_email>\Preferences
FloatChatFlashColor
A DWORD value (by default -1) which is the color used to flash the background of floating contact windows when a new message is recieved. By default, the background color of the window is used to compute a darker or lighter color. This is a COLORREF value.
A COLORREF value is the hexadecimal representation of an RGB in the form RRGGBB, where RR is the hexadecimal value for the red component, GG for the green and BB for blue.
eg: white is: FFFFFF
black is: 000000
gray is: C0C0C0
red is: FF0000
blue is: 0000FF
yellow is: FFFF00
etc
FloatHideTempo
A DWORD value (by default 8000) which is the delay, in milliseconds, used when floating contact windows are temporarily hidden when middle-clicking on them. The windows are automatically shown back after this delay expires. The range of acceptable values is 200 to 3,600,000.