Simply create a new SSIS 2012 project and right click on packages and add your existing packages one at a time.
That should do the job.
Here is what I did in Visual Studio 2010 Shell:
1. I copied a 2005 package to one of our dev servers.
2. I added it into Data Tools and now I can see the package in the Solution Explorer under Integration Service Project 1/SSIS Packages.
3. I then clicked on the project and went to the menu and did Project/Upgrade All Packages
4. It brings up the Package Upgrade Wizard and I click Next.
5. It then takes me to a Select Packages page but there are no packages.
Why is my package not being picked up the Package Upgrade Wizard?