A free conversion called mediacoder does a good job of transcoding most files from one format to another. Do a google.

Can't help with the software part of the question except to say if your editing program won't recognize and support the file type you are trying to import you may have to convert your source material to a file type the program will recognize and then edit or do whatever you are wanting to do and then when you render your project you can convert the result to the file format you need.
goodluck