Unless I'm missing something , you can't assign which decks you want to control with serato remote . For example, on controllers with 4 decks and you want decks 1 and 2 to be controlled by the hardware and decks 3 and 4 to be on serato remote , can't do it !
When you change focus from deck 1 to deck 3 on the hardware, serato remote follows the focus deck.