In response to this filer question here is what one clerk told us:

"It should not be efiled. You may only do this if the case is already sealed, or if you have an order allowing; you to file the motion under seal.

You may file it over the counter or through the mail and the document must be sealed inside of an envelope with a copy of the first page of the motion adhered to the outside of the envelope. The page that is outside of the envelope should only show the cause number, the style of the case, and the title of the motion – with filed under seal. We can file mark a copy of this front cover page and mail it back/hand it back for your records."

This procedure may differ by jurisdiction so this is a question you probably should verify with the clerk of court in the jurisdiction into which you need to file a motion under seal.