The rule fires when the amount is 500 or less, unless the bypass box is checked for the running user. Use the same pattern in any validation rule by adding the NOT condition.
How the hierarchy works
Salesforce looks for a setting for the user first, then for the profile, then for the organization default. A user value overrides a profile value, and a profile value overrides the default. If the organization default is checked, the validation is bypassed for everyone who has no value of their own.
Other options
Custom permission: assign it through a permission set and use $Permission.Bypass_Validation in the formula. It is easier to audit who has the bypass.
Custom metadata: good when the setting should be deployable between orgs.
FAQ
Can I use the same setting in Apex? Yes. Read it with Validation_Settings__c.getInstance().Bypass_Validation__c.
Is a bypass safe in production? Keep it limited to specific users or a data load, and switch it off after use.