All spells receive the option of Saving Throws, including Prayer and Bless. Creatures do not need to accept it. Objects automatically roll for a save.
In a bounded system modifiers overlap and (optionally) subtract. They do not stack.
It's actually easier in that you don't have to use arithmetic as often, but you'd still track each effect (which can be simplified with die trackers, etc.)
For example, Prayer for 1 minute grants +2 to AC & Saves. Bless grants +1 on Attack rolls for 1 minute. Traditionally these modifiers overlap and not cancel each other out as they granted similar effects (not different as they do here). If a Curse -1 to Saves were applied, then it would subtract Prayer's Save bonus to a +1. Alternately, as Prayer is the more powerful effect it could still remain fully in effect and the curse would only apply when the Prayer's duration ended. It depends on the system in use.
Note, bonuses and penalties can be applied anywhere, so you can Bless a person (ally, self, possessed during an exorcism), an object (holy symbol, weapon, statue), or place (shrine and so on).
I strongly advise they pump this to 24 hours as the spell is daily, then offer the craft spell Permanency at higher levels.