My plus toasts appear like your MSN toasts appear - not over the bar. Just try changing the sidebar position to float in the sidebar options then change it back to dock and see if this makes any difference.
You can just use Plus! notifications for when contacts sign-in and turn off the msn messenger notifications.
To turn on Sign-in notifications for plus Goto Plus-> Prefrences-> Notifications-> Popup Deafults-> and Check "Enable Messenger Plus! notifications when contacts sign-in".