It sounds like you're trying to use a MagSafe case on a non-MagSafe Qi charging pad. If the charging coils in the charging pad are not perfectly aligned with the coils in the back of the phone, it won't charge. Many older Qi chargers weren't designed to work with MagSafe, so it would make sense this is an issue with your charger.
I'd consider buying a newer MagSafe charger since you're completely set up to use one, including have a MagSafe case on your iPhone. They don't have to be expensive and you can find literally hundreds of MagSafe chargers on Amazon or your favorite retailer, including Apple or BestBuy.