With Gestalt, I've always used the sidebar for 'Fractional BAB' and 'Fractional Saves'.
That is the only way to really keep a Gestalt character in line with a normal character, in terms of their attacks and defenses.
You can then bring in mostly the correct Encounter Level / Challenge Level creatures and have the game run fairly smoothly, with minimal modifications required on your part.
If a monster relies heavily on 'save or nasty effect' abilities, each character is very likely to have all good defenses, meaning either bring in something two levels beyond what you normally would or reduce the CR/EL by two.
In my games, I've found that bringing in +1 EL/CR for 'doesn't rely on attacking a specific save' or +2 EL/CR for 'relies on targeting a specific save', to be a happy fix.
As in, my group is level 4 and I'd like a challenging encounter, that isn't likely to kill anyone if they play smart. Normally I'd throw an EL 6-8 (depending on their overall optimization level) encounter at them, but instead I throw 7-9 or 8-10 (again weighted by their level of optimization).
One simple fix, and the system works for Gestalt characters.
Sure you could go with additive saves, such as:
LV 01 - Fighter 1 | Wizard 1 ........ +2 Fort
LV 02 - Barbarian 1 | Wizard 2 ..... +2 Fort
LV 03 - Cleric 1 | Wizard 3 ........... +2 Fort
Then be a level 3 wizard, with +6 to Fortitude...
If you choose to go with additive saves, rather than fractional saves, that breaks the game system.
An even moderately optimized character is going to be almost immune to any game effect that allows a saving throw.
If I were to let you have an NPC spell caster (for an encounter), who is restricted to spells that allow saving throws... the challenge rating system isn't going to work against 'additive saves' PCs, who will essentially be immune to your effects, especially if they have Rogue2 or Monk2 somewhere in their build for Evasion.
Fractional BAB and Saves accomplishes this.
Full BAB classes (those with +20 BAB at 20th level) gain +1.00 BAB per level.
3/4 BAB classes (those with +15 BAB at 20th level) gain +0.75 BAB per level.
1/2 BAB classes (those with +10 BAB at 20th level) gain +0.50 BAB per level.
Until it's a whole number BAB rounds downwards.
But you take the better value, from your combined two classes, for each level.
So Wizard|Fighter and then Wizard|Barbarian, would take +1.00 (twice) as Fighter and Barbarian are both full BAB classes and therefore the better of the two values (Wizard being a 1/2 BAB class both times).
The fractional saves is a little more complicated.
If either of your (two classes) has a good save, that value begins at 2.00; if neither of your (two classes) has a good save, that value begins at 1/3 (or 0.33).
The Fighter | Wizard would then have:
Fort 2.00 Ref 0.33 Will 2.00
After the first level, you now only add the fractional value.
Going Barbarian | Wizard, you add:
Fort +0.50 Ref +0.33 Will +0.50
Giving you: Fort +2.50 (+2), Ref +0.66 (+0), Will +2.50 (+2).
Which is in line for any single classed level 2 character who received good Fort/Will and poor Ref saves.
You'd have to round 0.99 to 1, because we're actually adding 1/3 + 1/3 + 1/3, not 0.33 + 0.33 + 0.33.
It's really up to you (or whoever is running the game), if you (they) want a working mathematical assumption on savings/attacks/ac or if you (they) want to either modify each encounter depending on the defense attacked/save required (sometimes for each PC in the group... if one has stacked FORT to +12 at 6th level, while the others are closer to a normal +1 to +4) or just accept that the values don't work and that your (their) level 12 monster should be worthless, or worth very little (in terms of experience) for a group that has +12 to a saving thrown, when the system anticipates +3 to +5 for the saving throw.