Now, when you say you have a 2.1 setup, does that mean it's an actual receiver with two speakers and a subwoofer hooked up to it? (I had such a setup for a long time before adding the other three speakers.) Or do you mean it's one of those computer speaker things with a bass module?
Really the only way to hear the LFE channel is to use a digital cable (S/PDIF or HDMI) to bitstream the 5.1 ac3 signal to a receiver with Dolby Digital decoding. My Macbook has a combined headphone/optical mini output, so I'm able to use an optical cable with one standard side and one mini side to connect to my receiver and use 5.1 audio in DVD Player or VLC. If you don't have such a thing built in, an external sound card with S/PDIF (or multichannel analogue) output may get you what you need.
Moth3r is correct that the LFE channel is normally dropped when downmixing into stereo. Depending on the program and equipment, volume reduction schemes may be employed to prevent downmix clipping. Whatever dynamic range compression profile is specified in the ac3 signal will be acted upon to reduce peak volume, which is annoyingly non-defeatable on nearly all setups short of a full 5.1, but that does not apply in this case because my Star Wars mixes are specified not to use DRC at all. Some receivers, such as mine, may actually send the LFE into your left and right speakers if no subwoofer is present in the system, which can be either a good or bad thing depending on your speaker capabilities. Generally, it is better to let a real sub handle such strong bass signals.
If using an analogue stereo output, which it sounds like you'll be doing, then you'll want to use the stereo track for sure. The LFE will not be heard regardless in this case, and by selecting the stereo version you ensure hearing audio that is optimised for 2-channel playback. There is a possibility of phase smearing when downmixing a previously upmixed 5.1 signal to stereo again, due to whatever delay may be present in the rear channels, and as previously mentioned the volume may be reduced, so this is not particularly recommended, though it may not be as bad as all that.
Interestingly, I have found that playing the 1993 stereo mixes with a subwoofer turned up about 6 db louder than normal results in something that approximates having an LFE channel at times, since there is genuine low bass mixed into those tracks in some places, but you should never actually watch the films this way because you'll also get a huge increase in bass from the music and other elements that really shouldn't be amplified that much. (Jabba's voice is one example.) Unfortunately, LFE channels can't be sent over a stereo analogue connection, because it would result in ridiculous amounts of clipping were they to be added into the rest of the sound, creating truly hideous distortion.