So far I've haven't had any issue with using a debit card on Mog Station when I upgraded the account to Digital Collector's Edition. It's a Mastercard debit, too.
(If you have NoScript running, set it to allow
gcsip.com, their payment processor.)
As far as payment methods, I highly recommend using Crysta. It's hassle free and less of a headache. Just buy enough to pay out for 30, 60 or 90 days, and that's it. Set it and forget it... until it's time to recharge Crysta again.
Also, when you are at risk of having a chargeback because you had insufficient funds on a debit/credit card to pay for an account, you do run the risk of getting banned by Square-Enix. I've seen it happen years ago to another player, and it has happened recently as last month or two when it was posted on FFXIAH forums. Apparently SE doesn't take too kindly to chargebacks by your financial institution.
So, keep that in mind.