I'd go with DTS-HD for the theatrical DTS, and consider either LPCM or Dolby Digital at an appropriate bitrate for the 2.0 track. The advantage of Dolby Digital over LPCM is that you can set the surround flags on the encoder to preserve the surround that is matrixed into the two channels. I don't know if that can be done with LPCM.

It could be possible to do a similar thing with the 2.0 track with DTS-HD. There should be an option to create a stereo surround file, but how it would sound could hinge on whether Dolby and DTS use the same/very similar methods for matrixing the surrounds into the two channels.

You could preserve the DTS as LPCM if you really wanted to as the Blu-ray spec allows for up to 8 channel LPCM audio, but your 6 WAV's would need to be in a single multichannel WAV or RAW PCM file to do that. Any DAW that supports multi-channel audio should be able to export to these formats.