Dan,
I use a second plan view, one with the data and one for the pdf. If pdf plan view is active (view 'Title' not greyed out) when applying, it 'zoom extents' this view and the plan view on the data remains as it was (all it takes to switch active view is to hover cursor over view and scroll/zoom). This also makes it easy to pan/zoom about the two views to pick common locations to geo-reference. Make it even easier by rotating the data plan view to match the orientation of the pdf plot, when not North orientated (ctrl-shift middle mouse click/drag).
Rob