How do I pay them? With a check to the IRS and sometimes the state (this year the state paid me $50 - woo).
So the real question: How do I file them? With an accountant. Why? Because I own rental property and even if you can do business taxes without an accountant, you're still better off hiring one. Why? Because you can expense it to your business (i.e. write it off), and write off your personal taxes as well, as long as you follow the IRS requirement that you are only going to an accountant because of your business. The best part is I spend 1 hour doing taxes each year, and the last year I did them myself I spent over 30 hours just looking up depreciating asset schedules (with rental property, all expenses are paid over a period of time, so a 5 year depreciating asset needs to be deducted at 1/5 the cost over 5 years - I had to find some items in the massive IRS tomes for these at my local library) and about 55 hours total (investment income was about 75% of the remaining time - played the Wall Street Lotto a bit too much that year).
Bottom line: if you own a business, hire an accountant.