When I'm writing a query should I..

Use your real name -- they don't care about the pen name at that point. It can come up when you discuss representation.

Alternatively, you can sign your query letter as "Jane Doe, writing as Twilight Sparkle".

From now on, I'm signing all my correspondence as 'Twilight Sparkle'.

I've never heard it suggested that a pen name matters all that much for good or bad, unless you're doing it to write in separate genres. Do what you're comfortable with, I'd say.

AngelaT.Marie said:

Also... what's your thoughts on pen names? I want to do mine because I really don't feel like having my name mispronounced over and over. That and there's sentimental meaning behind "Angela T. Marie"

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If your real name is something people might have trouble spelling or googling (because it's either very common or very uncommon) a pen name can be helpful. Mostly, I think it's just personal preference or, as another poster mentioned, handy for authors who want to write in multiple genres.

This is probably understood already, but if you've published previously under a pen name, you do want to mention that to the agent at the query stage so they can find your work.

Always use your legal name or DBA (do business as) name.

To indicate pen name, use it in the byline. Your agent isn't stupid. When he sees "Title by X" and X isn't your real name, he knows it's a pen name.

With a query letter use your real name, always. However, a line about your pen name, but only if you have been published before under this pen name and are referring to your writing credits in the query.

Nathan Bransford had a really good explanation of when you should and when you shouldn't:

http://blog.nathanbransford.com/2009/12/whats-in-name-all-about-pen-names.html

My last name isn't the easiest to remember to spell. However, it's only four letters, and I pwn my Google results, so it was a no-brainer.

AngelaT.Marie said:

Also... what's your thoughts on pen names? I want to do mine because I really don't feel like having my name mispronounced over and over. That and there's sentimental meaning behind "Angela T. Marie"

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Make sure it's a name that's always going to have a sentimental meaning for you...like they suggest with tattoos . If you're 15 and your first boyfriend calls you the name, chances are it might not be that sentimental in 5 years LOL.