After trying to go all digital I've found that I really do still love to read and study my paper Bible, and I am sure that I'm not alone. There is no denying the great advantages that Logos offers though and I have no plans to stop using it. I find myself going back and forth between the two without any symmetry at all and it leaves me feeling that there is a lost opportunity for integration, somewhere, somehow.
At the very least I would like to have a quicker simpler way to add notes to what I'm reading and have some kind of "to do" reminder sent to me to remind me to add the notes to my paper Bible. I think that this may just be the tip if the iceberg though and that there may be a lot of great ways to integrate.
One last random point to bolster my idea; reading comprehension is just better on paper. A friend of mine is big on this so I did some quick research to undermine his position, but I couldn't honestly do it. The majority or research shows at least a modest gain in reading comprehension from paper.