Joakim,
If the graft has enough roots to grow on it's own I would be removing the rootstock altogether (you can then just grow it as a second Paeony. Technically herbaceous rootstocks for tree paeonies are supposed to be temoporary and removed after a few years. The herbaceous rootstock continues to grow underground (I have seen huge swollen rootstocks larger than a rugby ball below the grafted plant) and can eventually rot and kill the grafted plant above them. I think that for ideal growth the rootstock should be removed after 3 or 4 years, but the majority of people just leave theirs in place. A few years ago a friend and I investigated a shooting rootstock on an imported grafted plant (my friend did a few bits of importing, which is a laborious process through quarantine etc here in Australia) and we were able to get a couple of plants out the rootstock, plus a big healthy plant that was originally the graft. All grew on quite happily. Once the grafted plant has sufficient roots it doesn't require the rootstock any more, and as I said the rootstock can become a problem in the future in some cases.