State tax filing

my wife only has income from Virginia.  Should I file a joint federal return, but file separately in the NY return for myself since she didn't receive any payment from NY?   Not sure if the tax consequences would be the same if I file as (married but filing separately) so that NY only calculates my NY income w/o factoring her VA income when they do their calculation.  Or does it not matter whether I file jointly in NY or separately?

 

Also, just fyi, if i try to file jointly on both federal, it rolls over automatically as joint for NY state.  Turbotax advises to file one jointly as federal, and another mock federal as separate so that it doesn't flow downsteam to the NY filing as joint during their automatic data download from federal to state.  

  

I noticed when I filed jointly in the state, I have a refund of 500 from NY, but I paid 1500 in taxes from my paycheck.  Shouldn't I get most of the 1500 back since I'm a non-resident?  In their tax summary calculation, they seem to be totaling the amount taxed by NY based on the sum of my wife's (VA) income and my income (VA plus the NY backpay).  I just don't want NY to tax both my wife's VA income and my VA income.  I would like to only file for the backpay I received (not the VA income) when i file in NY separate.