Capture and Project properties are of course not always the same. However, in a sense, the Project properties are usually meant for relative newcomers to video editing. If you intend to burn a DVD, then the Project properties will usually reflect this. But not always. If you are capturing DV/AVI from your video camera, then your Project Properties will usually reflect default DV settings. So mixing in mpeg-2 video with DV video, with the Project properties set to DV/AVI, would normally suggest that the mpeg-2 might be edited and somehow processed into mpeg-2.
But of course this is not the case. In fact, you will find as you become more used to editing, that you can virtually ignore the Project Properties. The really important step is what properties are used at the Share > Create Video File step. For newbies, if the Project Properties are set to DVD properties, then all you have to do is select Share > Create Video File > Same as Project Properties. But if your Project Properties are set to DV, that will produce a DV file which will still need conversion to DVD-compatible mpeg-2.
So regardless of what you have in the project -- in your case both DV and mpeg-2 -- if you want to ultimately produce a DVD, then you choose Share > Create Video File > DVD. The project will then be processed into DVD-compatible mpeg-2, and Video Studio will ignore whatever the original Project Properties were. That is why I say that in a sense they are irrelevant.
Selecting Share > Create Video File > DVD will, however, produce a default mpeg-2 which will normally be high quality with a bitrate of 8000 kbps. This means that you will only be able to fit 1 hour of video on a single layer DVD. If your project is 90 minutes long, or 2 hours long, then you will need to use different conversion properties. If you do this often, then it is best to create a special template using Tools > Make Movie Template Manager. If you normally have 90 minute projects, then you would use a bitrate of 6000 kbps. You can also change the audio format -- if you use Dolby or mpeg layer 2 audio, this will mean you can normally fit a bit more video (around 10 minutes) on the eventual DVD as these formats are more compressed than the default LPCM audio. If you have a lot of 2 hour projects, you would use a bitrate of 4000 kbps. You will know, of course, that the lower the bitrate, the lower the final quality of the video on the DVD...
If you only want to change the mpeg-2 properties for one specific project, then instead of making a template, you simply choose Share > Create Video File > Custom. Then you change the properties using the Options button on the dialogue box which appears.
Before actually converting the DV to mpeg-2 as I originally suggested, you might want to first try converting your original mixed video project to mpeg-2 but turning off SmartRender, just to see if the audio problem persists. In the conversion, with SmartRender on, then Video Studio will be converting the DV but not the mpeg-2. It could be that doing so makes VS run a little out of kilter and the audio gets out of sync with the video.
But if the problem persists even with SmartRender off, then I would first convert the DV to mpeg-2 and then process the project using all mpeg-2 files. And again, you might want to think about turning SmartRender off if you continue to experience out of sync audio problems. If you are using high quality (i.e. bitrate of 7000 or 8000 kbps) mpeg-2 settings, two full conversions of mpeg-2 will probably not produce any degradation in quality which is perceptible to the naked eye. However, such degradation is inevitable with mpeg-2 as it is a lossy format. And the degradation in quality *will* be more obvious if you use lower bitrates...
