Hi Olivia,
Because so many of my genealogical lines overlap I keep everything in one computer program called Main File and I have paper version to mirror that.
Then I have files for each surname, and a very large pile of papers and post it notes that need to be processed. The files for each surname contain other data that might not connect to my specific line, if and when it does it is moved to the main file.
For name and place specific data, such as my one name study and one place study the material is in Excel and on paper.
My filing may be very behind, but I have always kept a research log and this is upto date, showing where I have researched and where I need to research next.