Ryan,
You can elect to have your LLC treated as a C Corporation or an S Corporation. You are suppose to do this within the first 75 days of the year or after creation. However, I have had good luck asking the IRS to treat the election retroactive.
I am hosting an event tomorrow on this very subject (entity selection and the tax effects). There are still two seats available.
Quickbooks can calculate your profit but does not have a tool for determining the required estimated tax payments. It is 90% of current year's tax or 100% or 110% (depending on AGI) of your prior years tax.

