The hunt for obituaries, vital records and family photos is the stuff that genealogists live for. The problem is that once found those records have to filed.
File - The "F" Word for Genealogists
I am not going to recommend one filing system over another. Whether you file your research by surname, sequential number, state or country the most important thing is to keep your filing up to date.
Like many people I research in spurts. I may have a few spare hours on a Saturday night and decide to run a list of names through a newspaper database. In a short time I may have 10-15 articles covering multiple surnames - now what? Here is the problem, I do not have a SOP (standard operating procedure)to follow. The trick is to set up a filing system that works for you.
If you keep an electronic and paper copy of a record, be sure to cross reference them.
Do you have family pictures that cross multiple surnames? In my case the Maish and Horton famlies married into each other multiple times. Instead of inventing a unique naming convention I file them under each surname. I may be wasting disk space, but I can always find the picture.
Surnames that cross families? I have Warren families in Houghton Michigan and Plano Illinois. The Warrens of Plano are originally from Maryland while Anton Warren of Michigan emigrated from Sweden. I highly doubt there is any connection between the families. In this example filing by surname would be very confusing. In my case I file these by the primary surname they are related to - Schultz/Warren/Plano and Johnson/Warren/Michigan.
Just Do It
No matter what filing system you use, the trick is to actually USE it. Do not wait a year (like me) and start trying to remember why this piece of information seemed important at the time. While it is a great memory test it is not a great use of your limited research time.