How do I correctly document my initial investment and any ongoing investment in my S-Corp?

Get QuickBooks, create a set of books for your company, and use them to document everything where cash changes hands. Every time you spend money on the company, save any original documentation such as receipts and invoices and keep them on file, with a "tracking number" that is echoed in your QuickBooks records of these transactions. Each transaction where you spend your own money should be recorded as you loaning the company those funds. How that 'loan' is repaid to you, as in simply repaid once revenues allow, repaid with interest, at what rate, or maybe these 'loans' convert into equity against others also spending personal dollars on the S-Corp. How the 'loan' is handled is an issue for the by-laws of the S-Corp. But overall, record every cash exchanging transaction in a real accounting program, with documentation on file that includes the original receipts and invoices. The whole point is being able to use those accounting books and supporting documentation later to prove cash investment to parties including other company partners, potential investors, and the tax man.

Also, an easy 'rule of thumb' to prevent one from piercing the corporate veil: never, ever use company checks, credit cards or petty cash for anything that could be considered personal or non-essential for the business itself. As far as spending your personal cash for the company's benefit? Feel free, there is nothing wrong with that; just keep good records. Also, the company has to give you something in exchange for the use of your funds. Gifting the company can cause problems too. So, just keep good records, and those records include the company owing you something in exchange for the use of your funds - even if it is just getting paid back. That is usually called 'material', it makes a difference, so must be recorded with documentation.

The easiest thing to do, once you get your Employer Identification Number, or EIN, is to open a bank account in the name of the company under the EIN, put your investment into it, and pay all business related expenses (and only those expenses) from that account.

As a practical matter, if you are a sole individual, the corporate identity won't provide much of a shield, and to the extent it does, creditors are generally sophisticated enough to make you personally guarantee the business debts.

The biggest advantage, as I see it, of establishing the business account is that certain qualified expenses can be personally deducted if you start a business. The amount is pathetic, and don't get me started on the government needing to do more to incentivize start-ups, but if you itemize, it's money on the table.

After opening the account, I would make my first company payments to a CPA, and a lawyer. Often, one can refer you to the other, and that can be a good thing if there's some mutual understanding. For example, the CPA I typically refer to understands, if I say it's a start-up, to take it a little easy on the bill.