I would prefer to ease into the new formation by practicing it until my starting QB will have a formation IQ of at least 70. Practice and use the old formation until your new formation is implemented.
However --- I did it the hard way on my Oklahoma team in Wilkinson. I was stuck in NDB and 4-4/Nickel and I wanted to go to Pro Set/3-4. I looked at my roster and liked my Fr and So class so I changed immediately and basically surrendered the season. I practiced 20+ minutes on the new formations, played my young guys a lot, and by the time my Fr were Sr we went undefeated, won the CC and Rose Bowl.
One coach to observe is Ebel. I've watched him take over a few teams and make the current offensive formation work while he practices his shotgun. He has done some pretty good transitions to shotgun.