It doesn't matter. As long as you have two Pokémon with different home locations, you have increased chances to get a shiny (about 1/1365 in generation V, I don't know if it was boosted in generation VI).
I haven't been able to find numbers for the Masuda method in Gen VI; however, I did find the mechanics for how it works in Gen IV and Gen V. It attempts 5 times in Gen IV and 6 times in Gen V to produce a shiny egg. The overall chance of getting a shiny was modified in Gen VI (1/4096, up from 1/8192). Therefore, I have predicted the chance of obtaining a shiny with the Masuda method in Gen VI to be about 1/683.083 or about .146%.
To show what this means, though, see
http://www.wolframalpha.com/input/?i=plot+f(x)=100-100[%284095%2F4096%29^%286x%29]+from+x%3D0+to+x%3D3000
this represents the chance of getting at least one shiny after x number of attempts. It's not close to 100% until about 3,000, and even then the chance will never be 100%. Yes, the equation in there looks a little weird, but Wolfram Alpha seems to be promising me that it's equivalent to what I wanted (which you can see at
http://www.wolframalpha.com/input/?i=100-100+(4095/4096)^(6+x)&lk=1&a=ClashPrefs_*Math-). Also, the graph looks right, as I did it a while ago with Excel. Without the Masuda Method, (excluding chaining based methods that I don't know much about), it should take about 15,000 eggs to be practically guaranteed a shiny.
Basically, it shouldn't take much more than 3,000 eggs to get a shiny, which seems to be consistent with what people have been posting.
Source: Bulbapedia
"The secret ID and Trainer ID byte words are first xored together, and then the first byte word of the personality value is xored with the second byte word of the personality value. If the xor of these two results is less than eight, then the Pokémon is Shiny. This results in a probability of 8 in 65536; simplified as 1/8192 (2-13, or 0.01220703125%), just as in Generation II."
"Prior to Generation VI, if E xor F is less than 8, then the Pokémon is Shiny. In Generation VI, the Pokémon is Shiny if E xor F is less than 16. Therefore, in Generation VI, the chance of finding a Shiny Pokémon is doubled to 1/4096 (2-12, or 0.0244140625%)."
"An internal marker on each Pokémon identifies their "home location", 0x17. If the game recognizes the two Pokémon in the daycare as having different home locations, then when an Egg is generated, the game will attempt to generate a personality value that results in a Shiny Pokémon up to four extra times in Generation IV and five extra times in Generation V.[2] "
(4 additional and 5 additional ---> 5 and 6
