I too use a spread sheet. I have all the MSC's I am contract with, when and how they pay (5th, 10th, 20th, 14 days out, Paypal, direct deposit, check, whatever). Under each month I put what I am owed. I have a column that has the amount that I have scheduled with the company but not yet done. When I put in the report, I transfer that amount to the receivables column for that month. When I get paid I highlight the column. Those companies that pay more than once a month, I highlight in a lighter shade until the entire amount has been paid. At the bottom I keep running totals of what I am scheduled to work, what has been earned but not paid and what I have earned year to date and paid year to date.
I keep track of mileage and nights away from home as well as expenses on another page. I break the expenses out into tolls, hotel rooms, office supplies, etc. for the tax man.
I know how much I need to make each month and the total receivables keeps me working. When I get a really good payday, it drops those receivables way down and I know I had better hustle to get that number back up there. Cash flow is all important so I will occasionally take some cheap shops just because of when they pay. I know I will need the money for some gas about that time....
At his point, I mostly work for 5 or 6 companies and do the odd jobs for the other 60+ that I am registered with to keep the cash flow steady throughout the month.
I file jobs by company and when I get paid I purge that file. I have a box that the reports get put into and every month or two I empty that. I have never not had the notes on a job that I have needed.
The main thing is to find a system that works for you and who ever does your taxes. I found I was spending a lot of time on needless bookkeeping exercises that I could better use shopping or having fun. This is my job and I have done as many as 100 shops in a week. Too much paperwork with the reporting as it is! I don't need extra hassles with accounting stuff.