Your post is a little confusing, are you saying you have a PPL(A) but have now started an integrated course to get a CPL(A) and IR(A)?
If this is the case then you will only be credited whatever the FTO feels has been covered enough, anything else you will have to repeat, as it says, at their discretion.
There is nothing stopping you pursuing a modular CPL/IR(A), as you already have a PPL(A) this is the first building block.