MSP430 how to make configurable ISRs in a module (Code composer studio C)
First of all, it is not meaningful to discuss these things unless you have some sort of program design. If you have a simplistic program of less than 1k LOC or so, then you might not need any design, it might be sufficient to just aimlessly hack away. 

For larger, professional programs, you will need program design:

You should place ISRs in the same file as the rest of the driver controlling that particular piece of hardware, because an ISR is part of the hardware driver. They should not be in main(), they should not be in some unrelated file. 

They should not be in some "here are all my ISRs" file unless you are forced to bundle them together because hardware or tool restrictions. You might have to keep the vector table in a file of its own though, unless its location is handled by the linker.

main() shouldn't fiddle around with ISRs. You will have an abstraction layer on top of the drivers and main will call the abstraction layer. This means you will have no tight coupling between the algorithm and the hardware, and also that you can easily replace the driver without having to rewrite the whole program from scratch.