There are three possible scenarios with DTS: DTS 5.1 tracks (which the 990 can process as pure DTS, DTS+Pro Logic IIx, or DTS+NEO:6), DTS ES Matrix tracks (which will probably be flagged to force the 990 to use DTS ES Matrix), and DTS ES Discrete (with will definitely be flagged and must be processed with DTS ES Discrete to get the rear surround signal). For the first (and most common) scenario, just use the "DTS" button to pick your preference (although you may need to use the "Dolby" button to get the DTS+PLIIx mode, I don't recall at the moment).

With Dolby Digital 5.1, you can use the "Dolby" button to select DD+PLIIx or Dolby Digital EX, but I'd use PLIIx. I only use EX when the DVD has a Dolby EX track that includes a flag forcing EX to engage.

Here's one bit of trivia to keep in mind: the old Denon you used offered a "DTS ES Matrix" mode that could be used with DTS 5.1 tracks, while the 990 offers DTS+NEO:6 instead for these cases. The difference is purely one of semantics. DTS changed their standards not too long before the 990 came along and restricted the ES modes to cases where the source track was ES encoded in some manner. For those cases where they had previously used "ES Matrix" for generating a rear surround channel from standard DTS 5.1 tracks, they changed to using NEO:6. The matrix decoding scheme used remained the same. I've always figured that the change was done to help NEO:6 compare favorably to Pro Logic IIx - before the change, NEO:6 worked only with stereo analog or PCM stereo sources. Also, not all receivers or processors allow Pro Logic IIx to be used with DTS 5.1 tracks - it's an optional aspect of the PLIIx spec.