With sink base units it is almost always necessary to go in for a bit of butchery to get the unit to fit in around the pipework. This may well involve removing part or all of the shelf (they invariably foul on the sink S-trap) as well as or notching out the sides, etc. On occasions the back requires so much to be cut away that it is best left off, although in that case I tend to add 3 or 4in wide upstands (white MFC or Contiplas) to the backs of the base shelf and (if present) the mid shelf. Whilst it looks neater, I prefer not to box in under sink plumbing on the grounds that you will probably need access to it sooner or later, especially if your stopcock is there. Whatever you decide, always take the time to seal any cut edge (including factory edges which aren't edge banded) with a waterproofing material such as silicone, lacquer, gloss paint, D4 PVA glue (which is NOT polyurethane glue, BTW), etc in order that when leaks or spills occur they don't get into the chipboard and cause to blow (swell)
As an aside I'd also recommend that you install isolators on the tap feeds, etc if you don't already have them, before installing the cabinet. Can make working on taps, etc in the future a lot easier, and at under £3 a pop for basic 15mm ones it's really a no brainer IMHO