No I don't mean Schedule D.
PAYE Income is assessed under Schedule E. You've asked where / if the credit for your PRSI paid on PAYE employment is, and what I'm saying is that it is ignored in the computing of your liability on the Notice of Assessment.
Lets say you had 50k of income on your P60, and 10k of rental income. And you've paid 5k in PRSI on your P60.
Your assessment will show total income of 60k. Tax is calculated on this, and you get credit for your PAYE paid.
PRSI will be calculated on Schedule D income of 10k (i.e. your PAYE income is ignored, because it's assumed to already have been dealt with through payroll).
It's not your accountant who's charging it, unless he's living in the 1980's he has tax software that he enters the figures into which computes the liability along the lines I just described! And likewise, the Assessment is generated by Revenue's software - if it's applying PRSI to your Schedule D (rental etc) income then it's because that is correct.