Married filing separately. I have to enter Spouse federal Total Income(if MFS and living together) - Is this our income together?

No, this is your spouses federal income. Include all the federal income your spouse had.

Are the federal wages same as total wages in box one of w2?

And AGI how do I find that out?

Yes, federal wages would be box 1 of Forms W2 for your spouse.  When your spouse completes their return the AGI can be found on line 11 of their Form 1040.  

And if we have filled out the joint Federal? which federal spouse AGI and total Income should I include in MA form? Her individual ones or the global ones of 1040 form jointly?

You're filing a joint federal and a married filing separate Massachusetts return, I assume.  In that case the spouse AGI is the portion of the AGI attributable to the spouse not filing in Massachusetts.