If upsample sounds better than bypass, I'd seriously consider using digital output instead of analog - you're using the 990's DAC's anyway when using upsample, since using upsample with an analog stereo connection yields digital-to-analog at the DVD player, analog-to-digital at the 990, upsampling of that digital signal, bass management, and digital-to-analog at the 990. If you simplify to digital out of the DVD player, upsampling at the 990, and digital-to-analog at the 990, the results should be similar - and with the simpler path (eliminating both the player's DAC and the 990's ADC) very possibly better sounding.

If you are using NEO:6 Music with DVD's, there are two possibilities that I'd suggest might be worth changing. First possibility: you are still using a stereo analog connection out of the player for DVD's rather than the coaxial cable instead. Second possibility: you are using the coaxial cable but your DVD player's digital output is set to PCM rather than bitstream (or raw, as some players label it). I say that because NEO:6 can only be applied to a PCM stereo signal or overlayed on top of DTS 5.1 to produce a mono rear surround - it can't be used at all with a Dolby Digital source, which is the standard audio format for DVD's. You need to make sure that you have your player's digital output set to bitstream/raw to make proper use of your 990. If you let us know what player you have, we can probably help figure out exactly what setting needs checking.

If your connections between 990 and 7500 are working (as they are, based on your comments), I wouldn't change anything.