I made some custom hyperlinks and would like those to be included in the Overlay. Alternatively, you could make an "Underlay" function that could basically import another PDF into the current PDF, but show it underneath the current drawings.
For the hyperlinks, try the Export/ Import Markup feature. Not sure if this will work but its worth a shot.
As for your other request, you should be able to do that as its own layer.
Give it a shot and let us know how it turned out