The round metal disc's fit between the end can and the link pipe. So you will have to unbolt the end cans, pull the holding springs off and fit the disc's.
When i first fitted my Leo's I thought the stock tune was good enough but I took it the Triumph dealer who fitted the Arrow under seat can Tune and the bike runs alot smoother and better. Only cost £27 here in the UK, worthwhile having it done.

The "12 Minute Tune" you have heard of is probably called that because that is maybe how long it takes the dealer to put the new map on. Here in the UK they charge 30mins labour.