I do what I'm doing right now.
Let me back up and explain.
I bought special Bibles for daily devotions. The fonts are legible and I like the margin size. While I study, the Holy Spirit reminds me, or just my recall of certain cross references that pertain to that passage. Sometimes He has me open directly to the place even though I don't remember where...then He brings my eyes to focus directly upon the verse. This is supernatural and occurs more often as I seek His will. It is a very emotional experience when I hear from God like this and my heart is overwhelmed with gratitude that He would take time to talk with me this way.. I write the cross references in the margins and any concise note that applies.
I use my Bibles so when they start wearing out, I ask my Father for a replacement. It is very specific and He always provides in an amazing way exactly what I ask for or better. After properly breaking in my new Bible, it is used side by side with my previous daily devotional. I transfer the appropriate cross references and my margin notes that I think will be helpful in the future.
For instance, an early Bible had blank pages in the back by the maps. I used those to record answers to prayers, miracles and notes on wisdom concerning the leadership positions I was given in ministry. I don't believe they were inspired, on the Bible is God breathed, but He provided special wisdom that I needed throughout life to hold meetings and prioritize properly.
When transferring cross references and such to my newest Bible, I go book by book until I get through the entire Bible, checking as I go.
The old ones go to my library when I'm done. Sometimes I refer to them on certain prayers or notes that didn't get transfered. I date the miracles that God performs in my life. One day I plan to publish them in a book. I have some already that are hand written rough drafts. I'm hoping that they will encourage the faith of others and especially my children if I should find that special princess to share my life with.