Alternatively scan everything and file it on your computer but remember to back your files up.
Send your bills via email and ask your customers to pay via BACS and email the remittance advice to you.
When I file the paper work for my business I file in date order but I do try to keep paperwork to a minimum. I do everything on line, my banking, my tax return, my VAT return and even my cattle movements.
At work we file by reference number but we are about to become a paperless office. Everything will be scanned in and sent to an in box. I will then distribute it electronically to my team. We have two screens per computer and can view the piece of correspondence while working on the account. Magic!
Good luck with your business Nucleus.