What I would suggest is to demux the source into the two streams i.e. audio and video. After demuxing, convert the audio using the several free or paid applications available(Ac3Machine, BesweetGUI[both free and both require BeSweet to be installed]) OR Sonic SoundForge 7(if you can afford it-Now owned by Sony which has stopped all support) OR Sonic SoftEncode(Also Sony-supported[I think]) to AC3 Stereo format i.e. 2Channel Ac3. Then do the same to convert the 2nd files audio to Ac3 2-Channel. Then use these 2 new audios to author the DVD using the many authoring applications available(my favourite-DVDLab) to DVD. You could also use DVD Author.
The reason it is easier to work with two 2-Channel sources is that it is very difficult to convert(upmix a 2-channel source to 5.1) and work with 2 5.1 audio streams as this requires an indepth knowledge of audio processing capabilities of the Dolby Encoder in order to not screw it up(I'll not mention the cost).
Hope this helps.
PS. Use the 2 audios and 2 video streams as they are(no need to mux them before authoring). Much easier to work with in the DVD authoring application.