[Jessica H (OP)]

It seems possible to "train" your bowels to empty at the same time every day.  How do they know what time it is?

[JnA]

Yes you can 'train' your bowels

this is essentially what people with spinal cord injury (SCI) do. They train themselves (with the help of laxatives and suppositories ) to evacuate at certain times three to four times a week. The benefits for an injured person are obvious.

However you are still a slave to the properties of the food you eat..  and evacuation isn't always well timed.

[RD]

"esophago-rectal reflex" and "gastro-rectal reflex".
 
If you eat at the same times every day your bowel motions, taking their cue from your gullet and stomach, can also occur at regular times of the day.