You can pay directly via the IRS website which is the recommended way or you can pay by check. Be sure to include your SSN on your check and the tax year.
Your quarterly estimated payments should cover your SE taxes of 15.3% as well as your ordinary tax rate to avoid penalties.
If you have health insurance through a non-employer, you may also be able to deduct your health insurance premiums as a business deduction. The Self-Employed Health Insurance deduction is limited to your earnings. Meaning, you cannot deduct more than you earned. This is also entered in the business expense section.
If you do not want to overpay, remember to calculate your deductions in with your expenses to determine your gross profit.
If you plan to take a self-employed health insurance deduction, be sure you still include your SE taxes on the amount you deduct for Health insurance, as this is still subject to medicare and ss tax. It is only exempt from your federal ordinary tax rate.
If you are using a program like QuickBooks Self-Employed and keep it up to date, it will help you a lot with determining how much you should pay each quarter.