We recommend using iTunes, but you can also use a program of your choosing. You must be aware that by default many programs may be set to encode using a compressed audio format such as MP3, AAC, or WMA. These formats are all "lossy", meaning they discard some portion of the audio information in order to create files that are smaller in size and require less storage space. While this is acceptable to many people as a final distribution format that listeners can store on an MP3 player, you probably want your CDs duplicated from a high quality, 16-bit/44.1K file format such as WAV.
Before ripping your CD, check the Import Settings by selecting Edit > Preferences > Import Settings (on the General tab). Make sure "Import Using" is set to WAV Encoder. You can also click the "Import Settings" button at the bottom of the screen that comes up when you insert an audio CD into your drive.
You can be sure the file is the correct type before uploading by making sure the file extension is .WAV.
Please see your iTunes help for more details on how to ensure your import setting are set correctly.