I did play around quite extensively with the various settings changing the bit rates etc on the audio output of the sound card. I decided to go with the recorded format for the music I have which was 44khz 16bit, the reason for this is purely that the Mac can transmit the audio through the digital output without performing any up-sampling. I don't think the soundboard in the mac is of a very high quality otherwise we would not be getting such an improvement in quality when outputting through the Dac Magic.
On a technical level when you increase the output sample rate to 96k the macs / software or hardware must up-sample your 44khz recorded audio to the 96khz output range. If the original file was not recorded at 96k samples per second then the computer must create 52k samples per second to fill the gaps. The main problem with this is that 96 and 44 are not easily divisible, if it was 44 and 88 all the computer had to do would be duplicate. In this case an algorithm would have to be used and I doubt the Mac would do this well. So with a 44k-88k upgrade you are not going to improve quality as the gaps are being filled with duplicates no extra data is being added, with a 44-96k upgrade you are potentially downgrading the quality as you can not directly split 1 sample in half to create two, this leads to errors and potential glitches in the music and will probably change the shape of the music.
Have you tried changing the algorithm on the DACMagic it does make a difference (little button on the front), I also had to tweak the bass and treble settings on my devices connected to the beoport as I found I had previously compensated for the lack of texture from the Macs analog out.
Luckily I could sit in the same room whilst I played around with the different settings, it was quite a tedious process.
One mans settings will never work perfectly for someone else as every speaker will reproduce sound slightly different as will its placement in the room, size of the room, shape of the room, etc etc. Ultimately if you like what you hear then thats what its all about, I swear it can become an obsession fiddling with the settings I changed my mind about 1 million times.