Personally, I'd put all the media from the old filter into the new one.
There's always a risk running two filters that the bacteria, for whatever reason, don't colonise the new filter, leaving you with an uncycled tank when the old filter is removed. Even if the bacteria do grow in the new filter, you'll more than likely end up with half of the bacteria you need in one filter and half in the other, again risking ammonia and nitrite spikes when the old one is taken out.