It is quite likely that you will never resolve those 2 chromatographically.
The reason you use deuterated materials as standards is because they are easier to sort out with a mass spectrometer. Benzene is molecular weight 78 (with 6 protons). Benzene-d6 is molecular weight 84 (each deuteron is 2, protons are 1). After you collect your chromatogram with the mass spectrometric detector, you sort the mass spec. data by the characteristic masses for each material. Thus, if (more likely when) they coelute, it doesn't matter.
If I were working on a method for trace benzene, at a minimum I would monitor m/z = 78 and m/z = 84 (benzene gives a pretty good molecular ion). You need to think along this line in developing your BPA method using deuterated BPA as your internal standard.