You describe two issues:
1) Audacity cannot be configured as default application for .aup files (via 
Properties -> Open With in Nautilus)
2) Audacity is not the default application for .aup files

Point one can be fixed in audacity by fixing the desktop file. This bug
will be fixed in the coming days when my next upload 2.0.1~rc1-2 of
Audacity to Debian unstable is synced to quantal. I uploaded the same
fix to precise-proposed (patch attached).

Point two can be fixed by adding 'application/x-audacity-
project=audacity.desktop' to /usr/share/applications/defaults.list which
needs to be done in desktop-file-utils.

** Patch added: "audacity_2.0.0-1ubuntu0.1.debdiff"
   
https://bugs.launchpad.net/ubuntu/+source/desktop-file-utils/+bug/1006610/+attachment/3203026/+files/audacity_2.0.0-1ubuntu0.1.debdiff

** Changed in: audacity (Ubuntu Precise)
       Status: New => Fix Committed

** Description changed:

  When I double click a .aup file it will by default open in Firefox.  I
  can manually right click it and go to "open with", but it should be
  opening in Audacity.
  
  Also, when one right clicks the file, then Properties -> Open With,
  Audacity is not listed as an option.
+ 
+ Part 1: Audacity cannot be configured as default application for .aup files 
(via Properties -> Open With in Nautilus)
+ Part 2: Audacity is not the default application for .aup files
+ 
+ [TESTCASE for part 1]
+ 1) Open Nautilus
+ 2) Right click on an .aup file, then Properties -> Open With
+ 3) Select Audacity as default
+ 
+ [TESTCASE for part 2]
+ 1) Open Nautilus
+ 2) Right click on an .aup file, then Properties -> Open With -> Reset
+ 3) Audacity should be the default

** Changed in: audacity (Ubuntu)
       Status: Triaged => Fix Committed

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https://bugs.launchpad.net/bugs/1006610

Title:
  .aup files open in Firefox instead of Audacity

Status in “audacity” package in Ubuntu:
  Fix Committed
Status in “desktop-file-utils” package in Ubuntu:
  New
Status in “audacity” source package in Precise:
  Fix Committed
Status in “desktop-file-utils” source package in Precise:
  New

Bug description:
  When I double click a .aup file it will by default open in Firefox.  I
  can manually right click it and go to "open with", but it should be
  opening in Audacity.

  Also, when one right clicks the file, then Properties -> Open With,
  Audacity is not listed as an option.

  Part 1: Audacity cannot be configured as default application for .aup files 
(via Properties -> Open With in Nautilus)
  Part 2: Audacity is not the default application for .aup files

  [TESTCASE for part 1]
  1) Open Nautilus
  2) Right click on an .aup file, then Properties -> Open With
  3) Select Audacity as default

  [TESTCASE for part 2]
  1) Open Nautilus
  2) Right click on an .aup file, then Properties -> Open With -> Reset
  3) Audacity should be the default

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https://bugs.launchpad.net/ubuntu/+source/audacity/+bug/1006610/+subscriptions

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