Set the sub to "Use" so that the LFE track stays there (rather than being mixed into the left and right channels). Based on what I see on page 54 of the HD-A1's manual, the crossover determines at what point small speakers get crossed over to the sub - setting the HD-A1's speakers to large should make the crossover setting irrelevent.

I'll be curious to hear your thoughts on the differences between the DTS digital output and the DD+ analog output.