Dear Miss Snark,
What is the protocal for submitting to agents if you're writing under a pseudonym? You have to have your own name on your mailing address for the SASE and so forth to get back to you, but the manuscript should have the pseudonym on it, because that's how it should be published, right? Or do you submit everything using your real name and then explain about the pseudonym after you've secured representation?
If you're JT Leroy, you just never tell anyone that you're really someone else.
On the other hand if you're Nora Roberts, you just put the new name in bigger letters on the cover of the book.
If you're using a pseudonym for non-elusive reasons, you just put Yours Truly, Brad Pitt (writing as Angelina Jolie) on your cover letter. You put Jolie/Sha Na Na Namibia as the header on your manuscript pages.
You will also need a one or two line explanation for why you are doing this. It can be as simple as "Google associates me with a bad crowd under my real name: Nicole Ritchie" of "I don't want my ex-spouse to know I didn't die in that yachting accident" or "no particular reason, I just like this name better than Sixxiou Queue". Pseudonyms are not a deal breaker but I will want to know your real name and why we're doing this in case you think you are Angelina Jolie or you are JT Leroy.