Amazon usually bill in arrears (no idea about Lightsail). In the general case even, it doesn't matter. What you owe Amazon is independent of whether your card allows the charge or not. You can run out of top-up VISA card credit but you may still end up owing Amazon money.
This applies to any other provider, too. What you owe the provider is what you contracted to pay the provider (eg. by consuming services, or clicking the "upgrade" button in a web interface). It is independent of them actually taking the money.