It's as easy as including those directives in your service definitions for the flaky links:
service_description Check Flakey Website
normal_check_interval is 5 (normal), but if a service criticals, nagios will disregard the normal check_interval and check again after the retry_check_interval. It criticals again, and again it will check after the retry_check_interval. Once max_check_attempts has been reached (in this case, 3) then nagios will change the state of the service to HARD (critical) and send out an alert. Just increase the retry_check_interval or max_check_attempts to raise hte time it takes nagios to change the state of the service.
As long as max_check_attempts and retry_interval are set in your service definition, they will override any template settings.