I'm Ann, from the team here at Shopify :)
I can definitely help with this! For starters, what I can tell you is that when it comes to PayPal and Shopify Payments, you can actually use both gateways in your store at the same time. Simply enable Shopify Payments by following the steps on this page, and then your customers will be able to choose whether they want to pay through PayPal or credit card when they're checking out in your store.
Some added pros to doing this will be that transaction fees will be removed from your store (you'll still have to pay PayPal's fees and credit card fees, you can see what those will look like on our pricing page here), and not only will you be able to use Apple Pay, you can also set up Shopify Pay! Learn more about it here.
The things you do need to keep in mind when you're making the switch is to make sure that your business follows the guidelines for Shopify Payments and that the payout times for Shopify Payments might be different from PayPal. For example, for stores in the UK, the payout time is 3 business days after the payment is captured on the order. You can see the payout times for other countries on this page in our Shopify Manual.
I hope this helps! If you have any more questions or concerns feel free to reach out to us on this thread :)
Have a great one,