Technically, if you received the checks they should be included as revenue to the corporation, even if the deposits are "in transit" and have not yet made it to the bank. If you do not count them as income in 2010, but still paid yourself your normal salary, then your company will show less net income for 2010. It is fine to deposit them in early January, just don't wait too long.
Thank you for your question. Please Reply if you need further assistance.
I think I remember someone saying that whatever is in the company account at the end of the year(profit) is taxed like it was personal income. Since I am not depositing the money until 2011, can it just go towards my taxes in 2011?
Then you must have an S-corporation. Even if you use the cash method of accounting, you still need to recognize the income in the year received. Per IRS pub. 538:
You cannot hold checks or postpone taking possession of similar property from one tax year to another to postpone paying tax on the income. You must report the income in the year the property is received or made available to you without restriction.
Here is a link to the Pub: http://www.irs.gov/publications/p538/ar02.html#d0e1136
No, you will not pay tax twice, you will just have a timing difference. When the checks are received they are income to the corporation, and when you pay yourself a salary you take a deduction. If the company has profit at the end of the year, then if you are an S-Corp, you will get a form K-1 with that amount for you to report on your income tax. This amount will then be available for you to withdraw later with no tax consequence.
Hope this helps,