If we work with SolidWorks 2006, no : I think it's the implementation in SolidWorks (add-in) that won't work, but we still have to be able to put them in the PDM thanks to the external software.
If you are using SolidWorks 2006 files with a newer version of SolidWorks, yes, as I indicated in my first answer.
Yes, your SW2006 files can be stored in the EPDM 2014 state .
On the other hand , you won't be able to upgrade them since to evolve them you will need a minimum SolidWorks 2013 and when you open these files for modification, SolidWorks will convert them for you.
If a 2006 file is opened in sw 2012 and read-write, it will be offered for saving and therefore converted to 2012. But if it is not registered, it will remain in 2006.
To be clearer: if you only work with SW 2012, no problem.
If you want to continue using some files with sw 2006, you just don't save them, but they can be in a newer PDM.