Since I started working for myself almost 6 months ago, I've had to get to grips with running a company myself, and I must admit that the paperwork was one thing that stopped me from making this move sooner! I've kept everything in order and I'd like to mention one tool which has helped me hugely with that: Harvest.
Each morning I log in to harvest and get an overview of my world:
This lets me see how the invoicing is going, and also the hours for the day/week/month ... which of course serves to remind me that I didn't fill in my timesheet yesterday :) The timesheet itself is great - super-simple, accessible, and even I've managed to keep it up to date. There is a week view which is simply a grid (client names removed and I'd like everyone to admire my new 40-hours-a-week lifestyle):
It shows totals for activity and day, and the grey hours are the ones I've invoiced for - you can invoice and "lock" the hours so it's easy to keep track of which have been invoiced and which haven't.
The invoicing has been a gift as well, rather than messing about with document templates, Harvest does them really nicely and I can see what's outstanding, overdue, paid, etc.
I got started with Harvest because their free option was enough for me to get started - when I began the business I had absolutely no clients and nothing planned so I didn't have any cash to spend, and importantly Harvest allowed unlimited invoices which was ideal for me as I was doing bits and pieces! Within a few months though I upgraded to a better account which only allows a few users (which is fine, there's one of me) but allows me to have more clients/projects and so on. So far, it's been a great tool and I thank the good folk across at Harvest for making it available :)