Keep it all! We have family records going back 100 years and I am constantly going back to find old information. That being said, there could be a whole lot of paper! You can keep it in that format, but I would suggest that you could scan it in a logical fashion and store in online is something like Dropbox. We have copies on our personal computers, backed up on external hard drives also stored in the cloud in Dropbox. There are other choices out there as well.
We use Excel to keep track of things, but there are software packages out there that are available for a fee. Up to you.
When we scan our records, we have set categories for each tract and name each similar file in the same way. For example, Deeds, Division Orders, Leases, Regulatory case documents, maps, exhibits, well information, etc. Always keep the original documents that pertain to title!