Yeah, that should do it. A designated stereo mix is generally going to sound better for two-channel than downmixing, so the most ideal sound is going to come from that version, but with a desktop setup such as yours it's probably worth the slight tradeoff in sound purity to be able to use the LFE channel. As long as you've got the external sound card set up to handle the 5.1 signal properly, downmixing but still retaining the LFE since it's multichannel analogue, you'll get pretty good results on the desktop system--strong bass and no dynamic range compression, at least for my mixes anyway.

Other films will still have unavoidable peak reduction, since Dolby made it impossible to get around the downmix DRC without having really expensive equipment. Using stereo or DTS if available can bypass this for some movies. It's not until a centre and rear speakers are added to the system that it goes away for 5.1 ac3, and nearly all commercially pressed dvd's have aggressive DRC profiles applied. This really annoyed me once I realised it--Casino Royale, for example, has a very powerful mix that impressed me a lot in the theatre, but became muted and dull in stereo at home. Finally getting the full system put together was the only way to make it sound as powerful as it's supposed to.