The below 5-page thread from last fall had a lot of information/troubleshooting.
http://www.dcurbanmom.com/jforum/posts/list/60/494892.page
I've pasted text of a specific post in that thread which was the most clear/helpful to me.
After getting DC one card
1) register card at Dcone site( email/ password )
Choose all options on where to register card( Dcpl,DCPS )
Click check eligibility , it should come back as " you are eligible)
Click " apply"
2) Now , go to wmata Smarttrip , use your existing acct or set up one and choose add a card
Add Smarttrip type number in upper right on back of DCone card, Give card a name
3) Now go to manage your smart trip, choose the card you just registered , go to bottom of page , you should see
Created ... Product... ( DC student free rail & Dc student Free R) on two separate lines with a date , ( 30 days from date you setup card)
You have to wait 24hours from setup to touch OneCard to a fare machine in bus or metro to activate card, must be done within the 30 days)
Now you are good to go , until next August!
-- Thank you for all this. I had gone to the DCOne site over the summer, but had never gone to WMATA. This school year he's only taken the bus, but he'd like to start going to school by metro. So, I just went through your tutorial and in step 3, the DC student Free R says its "in use" and the DC Student Free Rail Regular says "Not Used." Is that OK? Is it now set up for the Metro Rail?
--Yes but he should go to a Metro station soon and use it, which activates the card.