Generally speaking, how your business is organized is going to dictate how you will be paying yourself as a business owner.

Sole Proprietorship or Partnership
If your business is a sole proprietorship (someone who owns an unincorporated business by himself or herself) or partnership (the relationship existing between two or more persons who join to carry on a trade or business), the money you pay yourself is recorded in a draw account.  You are not allowed to expense a salary or any personal withdrawals made from the business. 

Instead of paying yourself a salary and paying employment taxes through Forms 941 and 940, you would generally pay self employment taxes on the net profit of the business at the end of the year. 
- For a sole proprietorship, this would be reported on IRS Form 1040 Sched C (or Sched C-EZ). 
- For a partnership, it would be reported on IRS Form 1065.

In addition, you will need to make estimated tax payments throughout the year if:
- you expect to owe at least $1,000 for the year after subtracting your withholding and refundable credits, or
- you expect your withholding and refundable credits to be less than the smaller of:
    -  90% of the tax to be shown on your annual tax return, or
    -  100% of the tax shown on your previous year’s tax return, covering all 12 months.

Corporation
Corporate officers who perform services for a corporation (either LLC, S-Corp, or C-Corp) are considered employees. As an employee of a corporation, you are required by the IRS to pay yourself “reasonable compensation”. Reasonable compensation in defined in Publication 525 Chapter 2.

This means that you must issue yourself (and any other corporate officers which perform services for the corporation) a paycheck and pay all the associated employment taxes on the appropriate schedule and file all Forms 940 and 941 as applicable. If you do not, the IRS may determine that adjustments must be made to the income and expenses of tax returns for both the corporation and an individual shareholder if the officer is substantially underpaid (or overpaid) for the services provided and you may be subject to interest and penalties.

Always double check with your CPA, of course, to ensure that you are recording things accurately for your particular business, but in general, the above is a good rule of thumb when figuring out how to pay yourself for the work you perform for your business.