In MogStation, go to Account Services, then click the button for "Recurring Subscription Setup". This should have tables with radio buttons to select what type of subscription you want (Standard or Entry--determines how many characters per world and how much you pay each month), and then how you want to pay (select a specific credit card or use Crysta).

Once you set it to Crysta there, it should debit your Crysta Passbook. I always add my UGC codes through the older SEAM page instead of the MogStation, simply because I'm used to it from my time in XI:
https://secure.square-enix.com/accou...?cont=account#

Once logged in there, I can go straight to adding Crysta with the big button there. Select how much I want to add, choose Ultimate Pay, then the UGC tab (may have to click the tab to see more options), put my code in and submit and I'm done. You can also use PayPal there as well by hitting that tab if you want.