If you have the dock showing, it will always be over top of normal windows. One of the reasons I keep the dock hidden. And on the left side of the screen because vertical space is at more of a premium.

There are probably third-party programs (aka hacks) to manipulate the dock in ways not possible through Apple's own preference pane or command-line prfs. Maybe someone else can chime in with a suggestion.

In the meantime you can search MacUpdate and/or Versiontracker for "dock" or similar to see what programs turn up.