First, you're not a "W9 employee." W9 is just a request for your tax ID and does not imply any kind of employment. You're self-employed and you may receive Forms 1099-NEC from your clients / customers. That is income you will report on Schedule C of your Form 1040 tax return. Schedule C is also where you will deduct legitimate business expenses.

Most likely you will run your business on a cash basis just like your personal taxes are, which means you record the income when you receive it, not when you send the invoice. In your example money received in January is taxed next year.

Estimated taxes are paid in April, June, September, and January. For your first year of self-employment, take the "total tax" from last year's tax return, divide by 4, and make that your estimated payment. Open an account with EFTPS.gov for making Federal payments and look into your state's online systems for making state payments.

You may want to open a separate checking account to keep your books separate, but you should not need multiple accounts. You should learn how to keep basic business books though.

One thing you might not be aware of is the self-employment tax. You now have to pay both the employer and employee halves of Social Security and Medicare tax.