"you just mean the total over-contributed should add up in my total income right? Regardless of if its from 2 different lines." Yes. The amount on line 1 of Form 1040 will be sum of box 1 of the W-2, box 2a of the code 8 Form 1099-R and the amount of the loss associated with the excess contribution reported on the code 8 Form 1099-R.
The payer of a Form1099-R is identified in the Payer information box on a Form 1099-R. If Fidelity is trustee of the plan, I imagine that the payer information would indicate Fidelity as agent for your employer, but that's only a guess.
