I've been charged with training photographers at my station on FCP X. We do quick turn around news and I was looking for a simple way to adjust levels and panning in one swoop. Usually I will put my reporters audio track and interviews on my primary storyline. Then I connect all of my b-roll clips. I highlight my all of my clips on the primary storyline, go to inspector, pan to the left and then uncheck all channels except for the first one(main mic). On the connected clips I do the same except I pan to the right and uncheck all audio except for the second one. Sometimes by doing this the volume control will be grayed out. Also my audio level comes down quite a bit. I do this to have that good Channel 1 and 2 audio mix. I could just go and individually adjust audio but this is run and a gun broadcast news so trying to find the quickest way to help our guys out.
I've had the same issue and here's how I worked around it. You have two options.
1. Instead of panning, consider creating roles for your separate channels. So all NAT, SOT, etc... is on one role. And all VO is another role. Then, when you export a quicktime, select the settings tab and then the drop-down menu for "Roles As:". Select "Roles as Multitrack Quicktime."
2. If your deliverables still require panning, I've found that setting the pan mode to "default" instead of "stereo" allows for the correct levels. For some reason, when panning left or right in stereo mode, the levels are lower. Pan Mode can be found under "Volume and Pan" it's a drop-down menu. So, the difference here is that it'll pop up the 5.1 mixer. Just drag the dot to the left or right speaker. It'll snap into position if you're worried about it not being precise.
The benefit to #1 is that you get to edit in stereo and don't have to listen to audio panned left or right (or change your mixer to center-pan). So you get to edit and mix at the same time. Plus, the final QT file has separated tracks, so none of the VO bleeds into the NAT/SOT track. I sent this out to a PBS news show and they were fine with it since they work from QT files now.