You have to bare with me as am relatively new at this - just bought a house last year, which is a very new house (building was completed in October 2009). There is already ample insulation in the loft, which is very thick and rises above the joists. I have bought some loft boarding from B&Q, as I just want to lay it down to store a few things.
Now, when it comes to putting it down, would it affect the effectiveness of the insulation if I were to compress it down to fix the boards to the joists?
Polystyrene cracks, breaks and is not robust enough to go in a roof-space or to be used for insulation. In theory if you compress your glass wool roof insulation its R VALUE (insulation value) will go down, but you will never notice it. Squeeze your insualtion is, pack it down, and floor the loft. The floor boards themselves do act has insulators - if they were sealed that is.
In view of this I will add that glass wool or mineral wool insulation is always in a constant losing battle with a/ General Winters Cold Winds, 2 / "roof envelope creation". Suffice to say just one open hole in a tiled roof negates the insulation value created. Buidling envelopes, air sealing, caulking, and correct ventialtion are the buzz worrds today. .
Obviously it will affect a effectiveness of the insulation. In addition to this, it can destroy the appearance as well. If it is a new house as you mentioned in your question, there is no need to add loft boards to the joists.