[RPG] When do you add the proficiency bonus

Those numbers are your overall modifier for that skill or saving throw. They include your proficiency bonus if you are proficient in them, otherwise they are just your ability modifier for that skill or saving throw. They're pre-calculated and listed on the sheet for convenience during the game so that you don't have to add up all your modifiers and Proficiency bonus every time that roll is made.

So if your example Cleric is proficient in Wisdom saving throws and has a Wisdom score of 15, their Wisdom saving throw modifier = proficiency bonus (+2) + Wisdom modifier (+2) = +4, which is the number that will be listed under Wisdom saving throws.

On the other hand, your Cleric probably doesn't have proficiency with Dexterity saving throws, and let's say their Dexterity score is 8. Their Dexterity saving throw modifier = no proficiency bonus (+0) + Dexterity modifier (-1) = -1.

There are other factors that can affect this calculation, such as the Rogue's Expertise feature, but this is the basic calculation that will be used in the vast majority of cases.

Your Proficiency Bonus is based on the total levels you have as a character, not on any one class.

Your proficiency bonus is always based on your total character level, as described in Chapter 1 [p.15], not on your level in a particular class. For example, if you are a fighter 3/rogue 2, you have the proficiency bonus of a 5th-level character, which is +3. (PHB p.163, emphasis mine)

The proficiency bonuses listed in the Ch. 1 table are the same as those listed in each class's advancement table. That is, the bonuses are identical across classes, so there's no differentiation between the "fighter 13 bonus" you mention and the "[anyclass] 13 bonus" or the "[class1] X/[class2] 13-X bonus".