My wife and I are separated. I now live in Florida she is still in Texas. We are filing married jointly. She does owe back student loans. Should I just file regularly or should I file with the injured spouse? Will I get my whole refund? If I wait and they do take my refund, can I file injured spouse then?

If you don't want YOUR MONEY taken for HER DEBT you file the injured spouse form WITH your tax return. Why wait until the money is seized and then try to get it back?