Nope. One clip per sequence then export all the sequences, or all clips in a sequence and that gives you one giant sequence.
However, if you haven’t changed the name in Premiere Pro from the original file’s name you can just drag the originals into Adobe Media Encoder and do it from there. If you have renamed them in Premiere just follow my last paragraph after transcoding to relink the Premiere files to the transcodes.
Using CS5.5 (don’t have 6 so some things might be slightly different), set the output directory in preferences, drag the first file over and set up your compression preset, drag the rest of the files over (they’ll assume the preset of the first file you did) and hit the play/start/submit button (whatever it’s called).
Once you get that done I’d just rename the original file folder with _original after it, make the transcodes the folder the same name as the original folder was and open Premiere – should relink to the transcodes that way without issue.
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Michael Hancock
Editor