Submit under your own name. The pseudonym is a secondary consideration that is determined at the contract stage. I've also read that one may submit using one's real name and in the byline use one's pseudonym.
Hopefully someone here has had direct experience relating to writing and publishing under a pseudonym and can give us a definitive answer.
The idea is to put your real name with your contact information in the upper left corner (name, address, email address, phone number), and then put your pen-name/pseudonym in the byline space in the middle of the page, under the title.
That way, the check should be made out to your real name and not your pen-name.
I've always done this, because that's what I've always been told to do, but some editors don't seem to understand things and I've received checks made out to my byline/pen-name.
So I still recommend that you format your manuscript as above, but also, when you communicate with the editor in the case of a sale, specify that the check should be made out to your real name, please, and make sure the editor understands that the name under the title should go on the published story.
In fact, it wouldn't hurt to ask that this be specified in the contract.