In Premiere CS6, I'm looking to export multiple versions of my sequence both with audio using various processes and unprocessed. Once I send a sequence to media encoder, can I continue to edit that sequence without affecting the state of the sequence that I just sent to media encoder (this is all before the encoding starts- I'm assuming once the process begins, it gathers all the info it needs together).

Or, do I have to send one version to encoder and wait for that encoding to begin before making edits to the sequence to make a different version?

... as an update, I just noticed that closing a project in Premiere that is currently encoding in Media Encoder, is ok, but then opening a new project in Premiere, causes Media Encoder to crash.

This is a bit of a bottle neck.

I'd be more inclined to make a copy of a sequence and carry out further edits on it, keeping the original just in case. Or nest the original sequence in a new one, and apply effects etc. if they're simple.

It shouldn't crash though. AFAIK, Premiere takes a copy of the project and saves it in your temporary files folder (or whatever the Mac equivalent is). As long as you don't actually change or delete source files it shouldn't crash or complain.

...Once I send a sequence to media encoder, can I continue to edit that sequence without affecting the state of the sequence that I just sent to media encoder (this is all before the encoding starts...

Or, do I have to send one version to encoder and wait for that encoding to begin before making edits to the sequence to make a different version?

I don't think you can do that. I'd follow Mike's suggestion and make iterations of your sequences - there's no overhead with that.

Regarding the crash - you might want to take it up in Adobe's forum and support.

You can edit without affecting what's getting encoded. Premiere creates a temporary project file and uses it to guide Encoder, which allows you to work in your current project.