An alternative is to estimate how much you might owe for the entire year, divide that by the number of pay periods in the year for your primary job, and adjust your withholding on that job to deduct an additional amount each pay period.
Your employer can easily do that for you, and it can be adjusted if part way through the year you need to increase or decrease the amount.
See line 6 on the W4:
http://www.irs.gov/pub/irs-pdf/fw4.pdf
Say you estimate your additional tax (income, FICA, and Medicare) will be $2400. You are paid twice a month at your primary job: 24 paychecks.
Divide $2400 by 24 = $100.
Give your employer a new W4 with $100 on line 6. An additional $100 will be deducted from each paycheck.
When you fill out your return, that additional amount will cover what is allocated to the three taxes for your side business.
If you find that you need to change the amount, just do a new W4.
Have you considered incorporation? You may find that helps with tracking expenses related to the side business and maximizes tax benefits for them. It's not really difficult or expensive.