If using whole or pruree add it to the fv after primary, about 4-5 days. Adding peptic enzyme will help clarity/filtration. 2 42pnd bags/10bbl is alot of flavor.
When using extract inject though sample valve or prv. The stuff is very viscus and will sit on the bottom of the TT. Probably why your flavor changes.
better yet hook up your pump to the seving port and recirc the beer though the prv (using a hose under the beer surface) for a while to mix. I've used this method with honey beers.
Brewmaster, Figer's Brewhouse
"Your results may vary"