I have run Ecobak bio pellets for over 3 years on my SPS dominate system. I think there is a balancing act that has to be accomplished for bio pellets to really be effective and not have the so called side effects, i.e. cyano and pale colors.
First off, You need a really capable and effective skimmer. As long as you have one that is highly effective you really dont have to worry whether the output of the reactor is going straight into the skimmer, just have it in the skimmer section of the sump is good enough.
Secondly, you need a good bio load of fish and you need to feed heavily. I truly think this is the best way for bio pellets to be effective for consuming no3 and p04. If you have the right balance of bio-load with the right amount of nutrients, your corals will never be pale in color. We have all been so programmed to starve our tanks in order to avoid nuisance algaes and high nutrients, but with bio pellets you have to do the exact opposite for them to really work.
Proper rate of tumble in the reactor is also key in controlling the side effects. Dosing MB7 or Microbe Lift Special Blend will help with cyano while using bio pellets.
Also, I dont prescribe to having to have super low p04 readings either in order for color and growth. my best rates of growth and best color has been with readings as high 0.10 on my hanna checker.
Here is my most recent thoughts on why folks say that bio pellets work well for n03 but not p04 in the long run. The consumption ratio theory of having to have n03 in order for the bacteria to also consume p04 is where the issue lies. I purposely feed heavy and I purposely dont change out my filter sock for 2 weeks. Whatever junk gets caught in the sock has plenty of time to rot and break down, hence the ratio of consumption is kept in line. Totaly my own theory but it seems to work for me, as I havent had detectable nitrates in years, but i know they have to be there based on my p04 readings always staying low despite my insane amount of feeding.