In my experience (limited) you will only get the L+R channels although this may depend if the LFE channel is present in the original soundtrack in the first place and if the audio encoder you are using even supports this (Mencoder/Avisynth/FFmpeg?? You did not say which you are using) and if you have a correctly configured amplifier (5.1) the .1 is the LFE which you have called the "subwoofer track"
What is the LFE channel you ask?
5.1-channel audio consists of five discrete, full range main channels (Left, Center,
Right, Left Surround, and Right Surround) plus an optional band-limited Low-
Frequency Effects (LFE) channel.
In contrast to the main channels, the LFE channel delivers bass-only information
(<120 Hz) and has no direct effect on the perceived directionality of the reproduced
soundtrack.(i.e. it depends on the angle of you sub)
I hope this answers your question!