In my non expert understanding (I was funded with a TAship for half the year and then had a fellowship in the fall) my W2 reflects my income and witholdings from my TAship, and the 1098 T is separate and reflects the fellowship funding.
However now that I write this I checked my 1098T from last year when I had no fellowship, and there is still "scholarship" money listed even though I didn't have a fellowship.
I'm officially confused too!
It would be highly unusual for there to be duplication on the funds shown on the W-2 and 1098-T, so:
1. You assume that none of the W-2 is included in box 5 of the 1098-T, unless your records indicated otherwise
2. You ask the school for verification