Capturing embedded video while also in the Video Express mode recording yourself.

How do you ensure quality audio when you're in the Video Express mode capturing yourself in video and then showing a slide in your powerpoint that has video which includes audio?  When I do this the final product is poor.  The audio in the embedded video in the presentation is terrible.

I checked the item properties, the clips from the Sony HDR-FX1 say 720x480. The clips from the canon camera are 19?0x1080. The footage on the Sony camera was shot in 1080i. Does this mean the footage from the sony needs to be recaptured? If so do you know what setting the easy setup should be set at? There is an Apple intermediate codec HD 1080(not sure exactly), would this be correct?
As a secondary question can you recommend what the sequence setting should be for these two cameras? I am working on a project that would use footage from both in the same sequence. On top of that

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