The other answers are good, and here is one practical approach to handling this.
First, the accounting capitalization (10m x $0.001 = $10k) is really irrelevant. In fact, we went for 10m x $0.0001 = $1k. Whatever you pick, your company after formation will show $X of assets (the cash in the back) and $X of shareholder equity. So far so good.
You then need to start spending money through the company. Rather than issue more shares, you can lend the money to the company; write out a loan agreement (probably something like a balloon payment 10 years out with 0% interest) and deposit the check.
If you're doing everything at the same time, and want to have $1k of shareholder equity with a total of $25k to spend, then deposit the $25k check and call it $1k to purchase the founder's shares and $24k loan.
In this case, your company now has $25,000 assets/cash, $24k liability (to you) and $1k shareholders equity: assets = liabilities + shareholder equity.
Hope that helps clarify things a bit...