My store is connected to Facebook by the Facebook shop and I have my product catalogue available on my Facebook as well as Instagram page, But while creating dynamic ads on Ad level I'm not sure which link should I enter in Deep link to website.
If I enter my homepage URL then customers won't be directed to that product or how does this work!
Deep Links are the ones that go to that specific product page. Deep Links also take a priority position when Facebook is transferring information, they'll contain complete data vs the homepage as a link will only receive very brief information through Facebook.
Tl;dr go with individual product pages
I've been in e-commerce ever since Amazons logo was a river ?.