This is what I would do (and I presently do), take a look at a Schedule C, (attached?). Set up an Excel spreadsheet, using YOUR headings that work and line up somewhat closely with the Schedule C. Weekly or sometimes more/less often, depending upon work load/time constraints, enter your info into the spread sheet(s).
My column headings are somewhat in the order of the Schedule C (part II), eg., Advertising (Line 8), Car expenses (L9), Insurance (L15), Rent (L20), Repairs (L21), Taxes L23), Meals (L24), Utilities (L25),etc.
I actual have a spreadsheet page per month for my business expenses (the thirteenth page totals all the columns and the next spreadsheet page just reduces the spreadsheet page to a one-page printout of my expenses (that I give my CPA).
Part I of the Schedule C would have your income info broke down (Excel spreadsheet again?).
Either you spend time trying to adapt Quicken, QuickBooks to fit your operation or create something that does fit by creating your own spreadsheet is the $64 question. Naturally, you can see that I prefer sitting up a spreadsheet that fits my operation, verses trying to adapt something that might not fit. I do enough of what are called 'work arounds' on the farm, I didn't need any more aggravation at the office.
One other tid-bit that I use, this might be a little old fashion, but it works.
Take 12 envelopes (at least 6" x 9"), put the months on them (Jan, Feb, Mar, etc.). Every time you get/pay a bill/invoice, put that receipt into the corresponding monthly envelope.
If you take this one step farther and write on the outside of that envelope the info, eg 'electric bill $22.57, insurance $325, advertising $112, etc.'. You might like yourself much better at tax preparation time. You don't need to dig for the receipt/info it's right on the outside of the envelope.
I do the first part of this (the 12 envelopes), being I use spreadsheets (one per month), I don't do the writing on the outside of the envelopes anymore.
No matter what direction you head good luck and keep good records, you will be miles ahead in the long run, IMHO.