Tell us a little more about your system. Skimmer? Which model? How are you running GFO? How much media? Replacement schedule? High capacity GFO? How long is your photoperiod? How many fish? Water change schedule? Cleanup crew? What are your nutrient levels for nitrate and phosphate? What kits are you using to test? How have you modified the TLF150 reactor?For your specific question, no need to kill the skimmer or GFO as the biopellets ramp up. My advice is to always start with 1/3 of the recommended amount of biopellets in the instructions. Most often, that's all you'll ever need. A little goes a long way with biopellets.
Also, once fully ramped up for the first time about 3-4 weeks in, I more often than not will get a bit of STN on some acros. Some acros will adjust to the quick nitrate drop well but some won't. For those that don't, I'm usually able to stymie any STN advance with just superglueing over the affected areas. I tell people not to panic as the corals will adjust to the new conditions and it just takes a little more time.
I'd recommend feeding the effluent of the biopellets directly to the skimmer using a simple PVC Tee, no glueing needed. Just buy a tee that will slide right over your skimmer intake nozzle and stick the tubing from the biopellet reactor into an open hole, leaving the last hole open so your skimmer can pull additional water from the sump.
Lastly, a gentle tumble is all that is needed. Just make sure they don't all clump together and not tumble. Don't blast them as you can release small fragments of solid carbon into your system and spur growth of nuisance algae, cyano, or dinos in the tank that will use the carbon.