For a single track, use the simple layout. Then you don't need a cue file.
Your audio file player is "stuck" because you need to turn processing on. At the top of Plogue, there is a row of bottons. The last one on the right says "off". You need to press that so it's "on".
Check out the videos here:
viewtopic.php?f=8&t=171and here:
viewtopic.php?f=7&t=164Re other software, that depends on what you want to do. If you are just going to playback multichannel surround from your PC you may not need anything else. If you want to dts encode (for a DTS music CD, DVD, AVCHD or BluRay) you'll need a DTS encoder and (for anything other than a CD) Audiomuxer (also from this site):
viewtopic.php?f=7&t=135Other cool and free software you might find handy:
foobar2000 for playback and audio file conversion
imgburn to burn CDs and DVDs
Exact Audio Copy to rip music from CDs