Retune
You'll definitely want to retune. I had my Jars installed by the dealer before I picked the bike up, and the service manager put what he called the "fattest" Triumph tune in the ECU. It popped like hell on decel, and after a week and a half, the inside of the pipes was still squeaky clean (running way too lean!). I got in on a group buy for a Tuneboy setup, downloaded a tune (thanks again Pig9r!) from the Trading Tunes forum specifically for the Jars and stock exhaust with adjustments to cure the decel popping and haven't looked back since. I'm still running the stock breather, but you can change the breathing setup for more power, and again, you'll want to re-tune to match the way the bike performs to the setup you have. BTW - I LOVE the sound with the Jars - very nasty. Hope this helps, look through the forums here, all your questions will be answered.
Mike