I think it's saying that if you use a check (American) instead of cash, you'll get credit for making your payment, but it won't be considered "really, truly" made until the check "clears" (meaning the bank approved the check) and the funds from that check are in the bank account of the person who received the payment.
New words, one handy idiom, and a 2-minute quiz — delivered to your inbox to keep your streak alive.