From what you printed, it does sound like they will withhold the taxes by reducing the shares that they grant you - so if they are still worth $2500 a year from now, the amount of shares that you will own a year from now will be equivalent to $2500 minus whatever your tax withholding would be. That is a one-time transaction.
I'm a little lost on the self-employment taxes...this has nothing to do with self-employment so no, there's no quarterly filing or anything.
If you make transactions in the stock during the year (sell some at a profit or a loss), the broker will send you a form at the end of the year for you to account for your capital gains or losses for tax purposes. If you lose money, you get a little bit of a deduction and if you make money, you have to pay taxes on it at the capital gains rate.
Welcome to the world of owning stock - it's not a headache, it's a nice benefit.