Its says that i need to uncheck the spouse box on w2, but i want to file married file separately is that correct?

[jtax]

If you file separately, then you don't put any of your spouse's income or deductions on your return. That is why TT is warning you that the spouse box is checked.

Each spouse does a return with his or her own income. Usually but not always this results in paying more tax. It is generally best to prepare all three returns (joint, each separate) to see what the least tax owed is.