Hi JarilynJewelry!
Once you start using Clover, you can connect it to QuickBooks via Commerce Sync. See the details about connecting Clover by Commerce Sync.
On our side, we have no control over your transition because Square and Clover are third-party apps. We're just a receiver of your data from these POS apps. You may need to disconnect your Square and connect your Clover account to avoid sync issues. It's kinda like starting new with a different POS. However, you can also try to ask Clover's support to know if there's a way to import your data from Square. That way, you won't have to redo your setup.
Please let me know if you have other questions in mind.