I'm going to counter all the other advice...
In this day and age, a lot of folks have already gotten out there on the web with their penname. You may have a blog, a twitter, be participating in contests...and of course, you want to start building your base as your penname.
There is more than one writer (myself included) on AW who query using an e-mail address associated with a penname rather than our real name...all you do is sign the email:
Firstname Lastname
(writing as Pen name)
The cover page of my manuscript has my full contact info in the upper left, and looks like this:
Firstname Lastname
(Pen name)
Address
Address
Phone
Email
and the title, halfway down the page says:
BOOK TITLE
by
Pen Name
Yes, the agent has to know who you are. But at the same time, if you've been tweeting at her and making smart blog comments as your pen name, you also want her to know who you are, know what I mean?
ETA: Also, technically, if you REALLY need to keep your writing persona and real persona separate, you could always file for a "Doing Business As" status, which does allow you to sign contracts and open bank accounts under your alias. However, for most of us, our agents will know our real names, and something like the above suffices. In my instance, I use a pen because at the same time I'm querying my debut, I'm also making my first strides in the land of academic journal articles, and I don't want people to google name A and find writing type B.
