I'm definitely sad I took so long to see this reply. I had my settings off so it didn't email me when I received a reply, fixed now but Thanks.
So I just grabbed the latest beta r323 and the additions sound enticing, at least the ones I understand

I'm going to start playing with the settings again.
One question about checking the keep dts audio in stream, I am running over hdmi and all but I don't actually have a surround sound system at the moment, the hdmi is just going into the tv and the ps3 outputs the sound in stereo. So does keeping that dts audio simplify things for my computer and the ps3 simply downmuxes it to stereo alleviating my computer from having to? Or should I just stick with stereo to begin with in the program? If so what bitrate, 128? 256?
Really thanks in advance. I'm trying to find that g-spot of transcoding goodness for my poor little mini.