Just a question, why so many ATM? You need the processing power?
I'm using 3 ATmegas for a reason,
1st Because I need MOSI, MISO, SCK pins (13,12,11,10,9) for a device
2nd I have a 2nd module that need same pins MOSI, MISO..etc exactly same pins so I can use 2 modules
on a single chip
3rd I need PWM pins, the 1st and 2nd chip got only 3x PWM pins, now you may say you can use pwm from both chips but I will better add a 3rd chip to use all PWM in a single chip single code.
My 1st and 3rd chip got already over 25kb of flash code so that's the main reasons why I need 3x ATmegas328 
As for connecting i2C, you put only ONE set of pullup resistors on the whole bus not 3 sets, if that was the question. anything 4.7k-10k. And use one power source and regulator for your electonics then other for heavy stuff like the servos.
I got that, 1x 5v 800mA regulator for I2C ATmegas and separated regulator for servos but the main question which still didn't got answer,
If I use 4.7k pull up resistors from A4 -> +5V, A5 -> +5V, what about the already integrated pullup resistors on the sensor modules that are connected thru I2C ?
Hi,
What is the application and how many sensors, servos, etc do you have, that requires 3 x 328's?
Hi Tom,
I can't tell you in details/specific components because it's a university project but i can tell you how many components I use, I got 7x modules which they are doing different stuffs they are connected directly thru digital pins and others thru I2C, I got 6x servo motors.
And because as I commented to Oscarko as well, I need 3x ATmegas328 (1st reason because I don't have others chips right now to use :D) and the main reason is because I go so many components that some of them use same pins, other sensors need other pins and cover my PWM's and that's why I need other chips to use PWM for servos..etc
Edit: If you like to hear the project I can post it in this forum after one and half month, it's my own project, my own budged so the university don't have legal copyrights on my personal project
I can make it free source after I finish 
How far over?
let me re-edit 7x modules, how far over what? how many I tested and connected already ?
I personaly tested and I always do that before building my PCB's testing everything on breadboard,
I already tested and wrote codes for 5x modules, left only 2x modules and few more functions to write and finish the coding/programming.
You do know that SPI is a bus?

Being honest?
I didn't knew, I thought the only Bus is the I2C A4,A5..... ow well nvm I will keep going with my project like that, I don't have time for modification, probably in the future, but even if I put in the same Bus the modules that use MOSI,MISO i already I'm out of Flash memory
My Master chip got already 23kb of data and my Slave2 which I got the other Mosi,miso module got 20kb of code, so I think it's kinda impossible even if I use them on the same chip as a bus, out of flash
memory.
It sounds like you are quite experienced at making PCBs and you have a reasonable workshop set up. What was the original question again?
Work shop?
are you kidding, I'm a student, people keep telling me that I need atelier/work shop to do what I'm doing but I'm doing all that in my apartament. My room is kinda messy while doing a project but after finishing everything is clean.
Well the only question left in this topic is about the pull up resistors
as I know and read I need 4.7k pull up resistors for I2C between ATmegas but what about the modules that I got as well in I2C ? I'm looking them and they got already integrated pull up resistors. Will that affect the communication?