Signing bonuses, for cap purposes, are prorated over the term of a contract. So for example, if a player signs a 5 year deal and part of the deal includes a $25M signing bonus, that bonus hits the cap at $5M per year for the five year term. However, the actual cash spent on that bonus is $25M in year one. So the cash over cap for that player in year one as it pertains to the bonus, is $25M in cash, $5M against the cap. Hence the term, cash over cap.
The more deals like this that a team structures in a given season, the more it will lift the cash spent over the cap number – a cap number that is predetermined by the league for ALL TEAMS.