Most apps now require them to be submitted online, but they normally allow for exceptions if circumstances require it. I'd shoot the school an email and find out exactly what they think.

One advantage of doing your application/rec letters online is the feature to "remind" your recommenders.

Many times, your recommender might be busy with other activities. Therefore, he/she might forget or push aside the task.

If you gave them the paper version, then you must constantly remind them in person. However, many online rec letter features allow you to automatically send a reminder email.

I found that useful.