Keep your business money separate from your personal money.

The easiest way to handle your business income and expenses is to have separate accounts.
I have separate checking and savings accounts. My business savings account automatically pays my self-employment taxes.
This is an important aspect of starting a business that should be done before income or expenses is incurred. Do not wait until you cannot tell the difference between your business and personal monies.

Your accounting methods need to be completely accurate and easy to find. This is an absolute necessity when doing your taxes or handling an audit. An accounting program like Quicken or a simple ledger can be used just as long as you fully understand what is coming in and what is going out.

After your business expenses have been paid with the income you have received, then you can make a check out for yourself. Transfer the money to your personal account and record it as owner payment.

Same thing applies if using personal money to pay business expenses, transfer the money from personal account to business account and record it as owner expense. You can pay yourself back when the income comes in later.