You are correct in stating that a person needs to have Green Card status for 3 years before being eligible to apply for naturalization (citizenship). Those 3 years can include the 2 years that he has held Conditional Permanent Resident Status. I would suggest that you go to www.uscis.gov and review the "Guide to Naturalization" that is posted on that website. The Guide is the official Immigration Service informational booklet, and it should answer many of your questions. I hope that this information is helpful to you.
As stated, the 3 required years start when his conditional green card was approved. That time overlaps your marriage. If he became a conditional permanent resident on 01/01/2009, he would have the required 3 years on 01/01/2012. The regualtions allow for him to file as early as 3 months before the completion of the 3 required years (i.e. after having a green card for 33 months). The 3 year filing is based on two foundations, first, that you remain married, and, second, that you file to remove the conditions of conditional permanent residency by filing to do so betwen 21 and 24 months after the conditional green card was approved.
He will need to be in the USA for at least 1 1/2 of the 3 years to meet the physical presence requirements. Once he becomes a US citizen, there are no residency requirements.