I am notoriously messy; it's a part of myself that I've just learned how to accept. But when I started freelancing, I realized I had to seriously overhaul my organizational skills if I wanted to be successful. Getting "freelance organized" means that while my bedroom may still be a hot-mess, at least my career isn't suffering.
I tried a variety of ways to keep track of my pitches, what I was writing, and who owed me money. First I kicked it old-school and wrote down all my pitches, where I sent them, and where they got rejected on a piece of paper. Needless to say that didn't last long. I would periodically forget to update the list, or worse: I would lose the sheet of paper amongst the mess that is my desk.
Next I tried Excel, but it was way too complicated for me (the last time I took a business class I was 15 and haven't looked back).
Which brings us to the organizational tool that saved the day -- or at least my sanity: Trello. Trello is an online project management tool that allows you to create "boards". Within the boards you can organize "cards" into "columns". The simplicity of this system means that you can use it in a variety of ways.
How I use it: I have a board for different types of writing I do, as well as a resource board full of websites that take pitches. For my writing boards I have five columns: To Pitch; Pitched; Writing; Editing; Owed.
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I then add cards for each writing idea I have, and can simply drag the card to the next column as I complete the pitching and writing process. It's really that easy.
When I'm feeling very organized I'll even use the comment tool to make note of where I have already pitched the idea and where it's been rejected.
If you're more organized than me you can label your cards as well. I tried to label the cards I'd pitched according to how long it's been since haven't received a response (green was one week in, yellow meant two weeks and that I should follow up, red meant a month without response). Although I couldn't stay organized enough for this route, you should still try it out, as it keeps you accountable for following up on pitches.
Once you've got your workflow in place, you'll be able to track everything coming and going. If you add a "to be pitched" column, you can even use the cards as scratch paper for your story ideas. When it comes to figuring out your money, the payment details will be invaluable.