Here is my process, which is very simple and has been working perfectly for me:
1. All receipts and invoices from my wallet, and mail, go to my "In Basket"
2. Log all my in-basket receipts & paperwork a few times per month into my bookkeeping software.
3. Put all logged receipts into a 6" x 9" envelope (one envelope per month).
4. Once I finish a month, I put that envelope into a box for that year.
So here is a supply list:
* CURRENT IN-BASKET: 1 letter sized "in basket" for my office; should not be too big, such as a box, etc.. .otherwise, you will be tempted to just let it pile up for a long time and then you will have a big job.
* MONTHLY ENVELOPES: plain 6" x 9" envelopes you can buy at any stationary store; just buy a box of them, they are very cheap and you will not run out for a few years. I always use a marker and write the "month' and "year" on the outside. Also, if you do a special project or go on a vacation, I would use a separate envelope, and label it like, "House Reno 20XX" etc.. or 'Trip to Hawaii 20XX".
* YEARLY FILE BOX: just a regular cardboard file box that you buy at a stationary store is perfect... then just write the year on the outside. Put all processed paperwork, monthly receipt envelopes, etc into that box after it is processed and dealt with. No sense in it piling up in your desk drawers or filing cabinets.... I find once it is this box, you can easily carry it out after the year is done and it is all cleaned up. No need to dig around your cabinets and desk for paperwork.
* BOOKKEEPING SOFTWARE: stay away from complicated accounting and bookkeeping software. Keep things simple, no fluff. The best accounting program for real estate agents I've seen is from http://www.moneyledgers.com
All you want is a simple way to create income and expense statement so you can see where your money goes and do your taxes each year, that is it.
* MUSIC: ... I really do not enjoy doing bookwork, so find something to help make it enjoyable. Play some background music, have your favorite beverage, etc... and remember DO NOT LET IT PILE UP.. or you will definitely not find it enjoyable.
Hope that helps!