So I just got married(to a RN), finished school in February 08, bought a house, and own 10% of a S-corporation. I dont want money back at the end of the year but dont want to pay in either. How many allowances shoud I be using?

S-Corp.  You need to be calculating your taxes, and either adjusting your w/h or sending in estimated payments accordingly.
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The withholding tables work very well for single people with 1 job (12 months constant income) who do not itemize.  Once you get married, income averaging pops up.  Your income has not been constant during the year and your probably itemizing.  Finally you will be taxed on the S-Corp income - which could drastically change the entire picture.  Running estimates is the only accurate answer.

+1 - See a tax professional (a CPA or at least an IRS Enrolled Agent)

If you don't want to/can't afford to do that, check out www.irs.gov/individuals/article/0,,id=96196,00.html

I pay in set amounts quarterly for the business side of it that has been determined by my accountant.

Now I just need to figure out how much I want/need taken out of my check.

Quoted: +1 - See a tax professional (a CPA or at least an IRS Enrolled Agent) If you don't want to/can't afford to do that, check out www.irs.gov/individuals/article/0,,id=96196,00.html

I just emailed my CPA on it. I just didnt know if there was a basic shoot from the hip method