I use vinegar, pretty much watered down vodka. I use 19.8ml a day spread out with lights are high and ph is at its max. both help to grow bacteria that will consume nitrate and phosphate. Vodka has more carbon then vinegar, vodka is 8 times stronger then vinegar. both have ups and downs. each system is different one thing works for me might not workas well for you.
the main problem I found with bio pellets is that you cant control the amount of carbon dosed to the system. maybe that's why they want the output to go into your skimmer? I know many people have used pellets without problems but I found they just aren't for me. With vinegar I found that sweet spot for my tank that keeps things in line without making my sps look pale. on top of everything its so cheap. People are always fast to change systems to the new trend that is going on at the time.
There are also Recirculating Reactors out now and you can always add a valve on the end of your output to control your effluent out to the skimmer. This is measurable ans controllable to prevent excessive carbon dosing from the reactor .
And even with a Bio-Pellet Reactor you can still dose Vodka (your choose) because it promotes a different strain of bacteria that's positive compared to Pellets, Sugar, or Vinegar.
There's a Coral Magazine Article Sept/Oct 2011 that covers this point in detail.
Also this is a informative Videos on Recirculating Reactors and how they work and why:
(Google this)
episode 107 LA Fishguys Bio-Pellet Reactors