I would like everything to play in it's native format
To play everything in it's native format (to the extent possible), leave "Output Encoding" set to "None" in DSP Studio "Output Format".
To send DSD tracks straight to your DAC with no conversion to PCM, set "Bitstreaming:" to "DSD over PCM (DoP)" in Tools / Options / Audio. If you have a DAC that doesn't support the "DoP" format, choose just "DSD" instead for this option.
If your DAC doesn't support the sample rate of one of the files you try to play, it will fail and Media Center will automatically try progressively lower sample rates until the track plays. Then it will set your Output Format sample rate table to reflect the selected sample rate. You can manually tell Media Center to convert those unsupported sample rates to one that will play OK and leave the others at "No change".