I just finished moving all my domains to them last week with their newest promotion, like $6 transfers or something.
Hello,
It does not matter which order they are listed, because when the nameservers are queried, they are queried simultaneously, and the first one to answer is assigned by the Registry to that particular query as "primary" at that point in time.
What this means is that regardless of how they are listed, the order of the listing does not determine which nameserver is queried first.
The order that the nameserves appear in the Registry is not up to the Registrar, and cannot be changed by the Registrar.
Snippet from a support email from Engine Yard regarding my questions of how important the order was since namecheap wouldn't let me specify an order per Engine Yard's instructions:
In the words of one of our engineers, it's importantish ;-)
Essentially d.ns.engineyard.com is the local primary, b.ns.engineyard.com is an offsite backup and e.ns.engineyard is a local backup. If you can't put them in that order don't worry to much about it, but if you can make d first that is preferable.