There are probably 100 different ways to do it, and it really depends on how you want to do it.
Whether you wire them to separate inputs or one input really doesn't make any difference at all. The software won't know which switch was tripped regardless.
The question is do you want do you want the limit switches to do? Do you want them to kill power to everything, or just tell the software that a limit has been tripped?
The safety circuit doesn't really do anything, unless you set up all of your components to properly use it.