I bought 3 of each new Commander deck and when I go to the mass input it only adds 3 of each card to my inventory however there are multiple copies of some of the cards in each deck.
For example when I do the mass input qty 3, deckbox tells me I have 3 Temple of the False God from C19, however I actually have 9.
Is there a way to change the mass in put to show one box at a time so I can put how many of that one deck I have.

Sadly, there's currently no native way to do this. The best option at the moment is importing the exact contents of the decks via a CSV file. Check out this related feature request / resource thread I started. It has been stickied to the top of the Site Discussion forum.

All you need to do is download the CSV for all 4 decks of C19 and import that CSV three times.

A couple benefits to this method over using the Mass Entry tool, aside from just getting the correct count of cards, is that all the commanders will be marked as foil, and the oversized card and tokens will also be imported at the same time.