I am adding this as a new answer based on new understanding that you may have a half size guitar.
That short of a scale might indeed work better with a higher tuning. But it may not work with the i-phone chord ap if not in standard tuning (not sure). Most 3/4 size and up will do well with standard tuning if the appropriate strings are used.
To tune to A starting with the fattest string (normally low E and technically the 6th string) use a chromatic digital tuning device (or phone ap) and tune A - D - G - C - E - A
Or try tuning to G for less string tension but still more than if in E.
Fattest string G then C - F - A# - D - G.
If you want to play along with your son with your guitar in standard tuning, put a capo on the 5th fret if he is tuned to A or 3rd fret if he is tuned to G.
The advice about stretching the strings from my previous answer still applies.
If your son maintains an interest (will take encouragement), move him up to a 3/4 or 7/8 size as soon as the budget permits. Keep in mind, that the guitar is not easy to learn and involves tons of practice, pain, commitment, dedication and desire. It is crucial for the student to feel a sense of accomplishment and be rewarded by success as early and often as possible.
Given the inherent challenges in learning to play guitar, there is a correlation between the quality of the instrument used to learn on, and the likelihood of success. I always encourage beginning students and parents of same, to spend the extra money for a better guitar to make the learning process more enjoyable and rewarding. Good luck - and please continue to support your son's musical journey. It could lead to a lifetime of relaxation, pleasure and creative expression.