My first year as a published author, I had one book out. My organization system consisted of saving the emails that CreateSpace, Amazon, and NookPress sent regarding my royalties and called it easy.
My second year was when things really got interesting. At this point I realized there was more to being a published author than just collecting payments and selling to my friends and family. That year I started having more costs than the first year, paying for bookmark designs, blog designs, promotional tours, etc. I also had two books out and I wanted to track sales in a little more organized manner. I began to create spreadsheets to track sales (which turned out to be a good idea once tax season arrived!)
I am now in the my third year of being self-published with four books published and have figured out a system that is working pretty well for me. The hard part now is constantly tweaking the system so that it doesn't become overwhelming as I publish more books and increase the cost (and sales) of my business.
I give you...my spreadsheets! If you would like a copy, just email me (sorry, but I'm having a hard time figuring out how to directly link it here) All of these were created using Excel so it is fairly easy to tailor them for your use. The workbook consists of a Yearly Profit and Loss sheet, Yearly Costs, Yearly Revenue, Yearly Paperback Sales, and Yearly e-book sales. I'm also working to form sheets that will track all of the sales per book (I have one right now, but it's not pretty, so I won't be sharing it quite yet).
Total Yearly Cost is just that, everything that I've spent on my books for that year. This includes covers, editing services, book orders, blog tours, and donations/give-aways. I have the Category table because I like to keep track of what I'm spending money on, and otherwise I will easily let the donations get away from me. I also include invoice numbers whenever possible, but that's probably an extra step.
This one is for my E-books, and I have a different sheet for each vendor (Amazon, Nook, etc.). Because the royalty payments don't happen immediately, I separate the sales and the payments. That way I can easily see when book sales increase/decrease, as well as keep tabs on when money is going into my account (and double check that everything is adding up correctly)
I love selling signed copies of my paperbacks, whether it is to friends and family or at book signing events. This sheet allows me to very easily see when/what I'm purchasing, as well as who is buying the book and any necessary information.
And finally, the big one, EVERYTHING. This sheet can get confusing quickly, but it's also great when I want to see all of my information in one place. I start with putting in my income from the previous year and then go from there. This also allows me to double check my revenue and cost sheets and make sure I don't miss anything. It's also very clear where my finances are each month and how my costs compare to my profits.