Ok. So, you're saying that I can use the knobs in the mixer to reduce the LFE activity?
How can I check to be certain my sound setup is consistent with Premiere Pro's new settings? If I change my own settings to match Premiere Pro's, would it simplify things?
The mp4 file I'm talking about would be the YouTube HD one under H264. I'm not sure if YouTube will support 5.1 or not, but that's essentially what I"m going for with the mp4. Now that I can use Premiere Pro, Audacity and Encore to created an MPEG with 5.1 tracks, it answers quite a bit, but again, I'm not even sure if YouTube will support it.
You set how much of each track should go to the LFE channel with this knob:

1) If you turn them all full CCW (Left) than you will have an empty LFE channel.
If you want to add effects only to the LFE channel then do it in Audacity, or buy Audition. Premiere and Soundbooth won't let you do that.
2) No matter what you do in Premiere, mixing, setting hardware settings, etc., Premiere will output the file correctly. All the tracks will be interleaved in the proper order. Premiere just doesn't display the order visually, the same way as other programs, or the way the file format dictates. The hardware settings in Premiere ONLY make the sound come out your speakers correctly, they don't affect file creation.
3) YouTube does have surround sound files on it, but I can't get them to play with surround sound in my browser on my system. I'll try and see why.
Elevator music........pause........hmmmm.......I'm hungry..........ahhha!!!
When you export from premiere to make a surround file for YouTube, you don't have to use the Audacity workflow, unless you want to add something to the LFE channel. Simply Output the file from Premiere in the H.264 format and select, for example, "YouTube widescreen HD" as the format. Make sure you set Output Channels to 5.1. Premiere will export an mp4 file.
Now you may have noticed that you are no longer in AC3 format, but in AAC. That's why you don't need the SurCode plug-in.
Well, as they say in Italy "Now we have a whole 'nother tomato to think bout."
The track order for an AAC file is not the same as an AC3 file. As a result, the track order displayed in Audacity will change depending on what kind of file it is. The format of an AC3 and multi-track Wave are the same, but an ACC file is a different format.
Remember the "Correct" track order for an AC3 file, L,R,C,LFE,LS,RS
The LFE track is the fourth from the top.
Here is what Audacity will display for an AAC file: C,L,R,LS,RS,LFE
That is the top to bottom order of the tracks.
So if you want to add effects to the LFE channel of an AAC you need to put them on the bottom track (track 6).
Now, optimally, we would like to export our LFE modified file uncompressed out of Audacity and import it back into Premiere, throw it on the timeline, mute the other tracks, and make our final mp4 file output from Premiere.
However, Premiere doesn't like the Audacity uncompressed wave file. I've tried multiple formats and I can't get Premiere to accept it as 5.1 surround file. It will import it, but it sees it as 6 mono tracks. So it will lay them all out on the timeline in 6 different mono tracks. That won't work because now we are back where we started with an LFE track with no way to assign it only to the LFE channel in the mixer. Again, that's because Adobe designed it wrong.
So what to do?
Unless I can figure out a way to export an uncompressed surround file from Audacity, in a way that Premiere will accept it as a 5.1 surround file, you are going to have to export from Audacity in the AC3 format, import that into Premiere, drop it on a timeline, mute your other tracks, and make your mp4 file.
That will work, but you are compressing twice, not the best thing to preserve quality. One thing you can do is export the AC3 file from Audacity at the maximum bitrate (640) to minimize the loss of quality, then set whatever final compression in premiere to your liking. It will probably sound fine that way. It's really the only solution for now if you want to modify the LFE channel.
We don't have this dual compression problem when we make a DVD because we put the AC3 file right into Encore, we never have to take it back into Premiere.
Have I earned my 10 points yet for the correct answer?