You can merge the scribbles with the PDF file. The iliad comes with some companion software to do this, but I never once got it to work. There is a community merge program written in java that works really, really well. You can even tell it to only produce output that contains pages that have scribbles on. This is very handy when proofing docs, etc.
See this thread:
https://www.mobileread.com/forums/showthread.php?t=9535