In addition to paying the tax on investment income, which is either 2 percent or 1 percent, foundations have to pay quarterly estimated tax payments. Typically, they anticipate what those payments are. If you’ve underpaid it, you need to rectify it, and how you do so really depends on how much you’ve underpaid by.
If you’re grossly and intentionally underpaying it consistently, you will likely incur penalties, just like you do on the individual side. So, estimate your payments as accurately as you can, keep up with them, and you should be fine. But, if you’re consistently paying them low, and it looks like you’re doing it deliberately, penalties will be imposed.