Make a small inventory of what each app changes: scripts, popups, structured data, metadata and access rules. Keep one owner for each feature; for example, avoid two apps generating competing product structured data or two overlays covering the same mobile controls.

Establish a baseline on your home, collection and product pages. Then enable one feature at a time and check mobile usability, page responsiveness, product variants, cart and checkout. Compare the same pages and devices before and after each change. Test theme-specific changes in an unpublished copy, while checking whether app settings apply store-wide.

For Shop Guard, verify that your protection rules still allow legitimate shoppers and intended crawlers. For Sales Pop, keep notifications away from the cart controls. If you share your theme and the exact features enabled in each app, the likely overlap will be much easier to narrow down.