Perhaps better worded as
Class A + Class B = Class C
Fighter + Monk = Fighter Monk = fast save for all 3 saves
Class D + Class E = Class F
Monk + Ninja = Ninja Monk = Fast saves for all 3 saves
...
Should thus be +4 all saves (based on how other multiclassing works, And +1 BAB from the first lvl but +0 from the second again based on how other multiclassing works
But that's not how gestalt works, at all. You choose two classes, and pick the best abilities of each at each level. And you can't take the same class on "both sides" throughout your advancement. The easiest way I've found to do it is by separating your classes with a double slash (//). Once you take a level in a particular class, any time you take a level of that class again, you gain that class's next level abilities. So, in the original example, the character has 1 level each of fighter and ninja, and 2 levels of monk, you list your class like so: Fighter 1//Monk 1. Compare the abilities of each class, as follows:
Fighter 1 // Monk 1 = Ability
BAB +1 // +0 = +1
Fort +2 // +2 = +2
Ref +0 // +2 = +2
Will +0 // +2 = +2
HD d10 // d8 = d10 (10 hp since it's 1st level)
Skill 2+Int // 4+Int = 4+Int
At second level, you want to take a level of Monk and a level of Ninja, you do the same thing, then add the results to the above, like so:
Ninja 1 // Monk 2 = Ability
BAB +0 // +1 = +1
Fort +0 // +1 = +1
Ref +2 // +1 = +2
Will +0 // +1 = +1
HD d8 // d8 = d8
Skill 6+Int? // 4+Int = 6+Int? (Use the ninja's skill points)
You then add the totals for a character sheet that looks like this:
Fighter 1/Ninja 1//Monk 2
BAB +2
Fort +3
Ref +4
Will +3
HP 10+d8+(Con*2)
SP 10+(Int*2) [Max rank=2, all fighter, ninja, and monk skills are class skills]
All special abilities of a level 1 fighter, level 1 ninja, and level 2 monk, i.e. Fighter 1 bonus feat, Monk 1 bonus feat, Monk 2 bonus feat, Improved Unarmed Strike (free w/ Monk 1), proficient with all armor and simple and martial weapons, etc, etc.
If we follow your plan, everyone should take monk at every level, b/c they'd end up with base saves of +40 across the board at 20th level. Fighter/Monk, Ninja/Monk, Wizard/Monk, Paladin/Monk, Sorcerer/Monk, Rogue/Monk, Gunslinger/Monk, Barbarian/Monk, Ranger/Monk, Summoner/Monk, and Bard/Monk don't all combine to give you base saves of +22 because they all count as "level 1" of a multiclass build. That would make gestalt even more broken than it already is.
Let's say we add a third level and choose to add Ranger 1//Monk 3. We do the same thing as before, compare the benefits and take the best:
Ranger 1 // Monk 1 = Ability
BAB +1 // +1 = +1
Fort +2 // +0 = +2
Ref +2 // +0 = +2
Will +0 // +0 = +0
HP d10 // d8 = d10
SP 6+Int // 4+Int = 6+Int
Our character now looks like this:
Fighter 1/Ninja 1/Ranger 1//Monk 3
BAB: +3
Fort: +5
Ref: +6
Will: +3
HP: 10+d10+d8+(Con*3)
SP: 16+(Int*3)
You've also picked up all of the level 1 abilities for a Fighter, Ninja, and ranger, and all of a Monk's 1-3rd level abilities.