Currently the IR questions are a subset of the ATPL questions, in other words exactly the same questions as the ATPL in some areas, other areas are excluded. I hear from the CAA, however, that EASA are trying to produce a bank of completely new questions for the EIR and Modular IR(A), this apparently is what is holding up the introduction of these ratings.
The general advice for aeroplanes, not helicopters, is that unless you are confident you will not need ATPL theory you should do the ATPLs rather than the IR exams even though it is more work initially. This is because as RTN11 says (1) you need valid ATPL theory to even fly as a first officer on most multi-crew aircraft and also because (2) if you do only the IR first, then decide later you need ATPLs, you need to do all the ATPL exams from scratch including the ones you already passed for IR.
If you entered for an ATPL course and then elected just to do the papers that cover the IR exams you can. There is a question mark over whether an approved ATPL ATO can sign you off for the (identical) IR papers without approval to teach IR courses, its one of those details that they didn't really think about when Part-FCL was formulated. The quick way around it is for the ATO to also get IR approval. I say quick, but the CAA are snowed under with approval applications at the moment, and ours is in the pile. If you are in a rush CATS do an IR course, as do Ground Training Services at Bournemouth.