When using the USB input of the HD3, what sample rate and bit depth should I set my system to?

The HD3's USB interface handles up to 16-bit, and sample rates up to 48kHz, though the bit-depth will be padded internally to 24-bit. Your system will generally default to these settings when you hook up the HD3. If you mainly use 44.1K files, you might set this as the default in your system to ensure minimal sample-rate conversions. Many system players like JRiver and Amarra will default to the proper sample rate automatically.