Melissa,
I am the caregiver to my wife Pat and she also has a PEG tube.

Based on my experience it is essential that you flush the PEG tube each day while he is still eating solid food by mouth. It's normal for food to come up the tube so you'll need to keep it flushed.

Second, they have an On/Off valve that goes into the end of the PEG tube which avoids the need to use the flapper valve on the end. Contact the doctor who put in his PEG tube and get one of the on/off valves. In Pat's case it was the Rad-Onc office that had these valves. Life will be much easier this way. You will avoid the leaks, not to mention the stomach acid. Good luck.
Walt