Thank you for your query.
If your GP is suspecting hypermobility in your son then he should be shown to a pediatrician
for confirmation and necessary management.
It is very common for joints to make the "clicking" sound and you should not be worried about it. Let the child move himself while crawling and he shall learn the technique on his own. You need not worry about a correct position for him to crawl.
I hope I have answered your query to your satisfaction.
Wishing your son all the best.