I can only see a couple of Shopify customers showing in the program even though I know more have bought than this,please advise?

Shopify have two types of customers > guests and those with accounts, 

The reason you are seeing less will be because those customers do not hold Shopify accounts. Only those with accounts earn points so we don't display the guest in LoyaltyLion.

*You can tell your customers this and it's a great way to encourage them to create an account*