My recent experience is that everything that occurs in a in-person/mail submission must occur in an internet submission.
In other words, all signatures, disclosures, etc. must be in place. The one exception is the disclosures that do not need to be signed (such as CHARM booklet) can be provided online as long as the customer cannot get around them.
This is kind of a general response, but should point you in the right direction. If you need more specifics, feel free to PM me.