If your accountant has requested additional documents or information, you should provide them with the information as soon as possible. While an extension gives you an additional six months to file, it does not mean you have to wait an additional six months to file. You can always file any time during those six months. For instance, you can potentially file in May instead of waiting until October.
You should also take the time to make sure your books are in order (if not already done), and track down any business expenses you may have forgotten about, which can potentially result in valuable deductions.
If you anticipate owing any taxes, you should make a payment with the extension to avoid any IRS interest and penalties. If you overpay the estimated amount, you typically would get a refund for the overpayment when your file your tax return. Your Tax Advisor can assess this for you.
In addition, you should discuss with your Tax Advisor, any State implications (if any). Each state may have their own special rules regarding tax extensions and estimated tax payments.