If a player has bonus money on his contract and you extend the contract. you still owe him the previous bonus money on top of the new bonus.
Let's say your RB is on the last year of his rookie contract and he is due a $5 million bonus. You extend the contract 6 years with a $60 million total bonus of $10 million a year. That player's new cap number will reflect a total of $65 million in bonuses, the $5 million from the rookie deal plus te $60 million from the new deal.