Yes, it will stop and alert you to change it if you're in the middle of a print. I find the best way is when I'm printing and I know it's getting extremely low, I watch the screen and when it gets down to the last 5mls or so, I will press to replace inks myself instead of waiting for it to completely run out. When it does completely run out, it seems to take longer to start back up and I have noticed a slight color shift from the heater and such.
Note: If you're not there to swap the cartridge to a new one within a certain amount of time (sorry, don't know exactly how long that is), it will cancel the job.