There is no complete way to get the architectural background (halftone/gray) to plot beneath the MEP work, as of Revit 2010. However, there are a few things you can do to attempt to get a better result.

First, make sure your sheet views are set to Hidden, not Wireframe. Typically, MEP users will create views that are wireframe for performance reasons. But Wireframe wreaks havoc on plot order.

Second, if the first approach is not enough, you can try the Raster printing mode rather than the Vector mode. Personally, I find this to be unsatisfactory, but there isn't much we can do. The factory doesn't seem to be very responsive on this issue.

Third, there is nothing you can do about linked annotations forcing their grimy way to the top, so stop trying.