Yes, limiting P and N will cause the other to not get absorbed as efficiently. However if you feed your tank a good quality food, you will always have some N and if you throw some flake food in now and then you will have P, which should solve the issue. So the bottom line is that you should be able to control N and P absorption via proper feeding when using a scrubber.
pskelton:
That is totally awesome. Dropping 60 ppm in 2 weeks from a brand new screen! Did you do water changes also? I wouldn't say that it would necessarily be directly attributed to the scrubber 100%, because at some point the nitrates getting released from the substrate should have slowed down, so time will tell.
As for the skimmer, if you do decide to pull it, do not pull it that soon. Wait until the N and P are down to low levels, and then leave it running until you are comfortable with the stability of the tank. Any change in filtration, even the position of rockwork in the tank, will throw the system into flux, which is generally what you want to avoid. So make changes very, very slowly and let the system adjust to the new 'set point' before phasing anything out. You might consider things like turning off the skimmer one day a week, then 2, and so on.