Is there any way to make rules on the import ?
That's a feature some of us would love to see, but it's not here yet.
In your situation of creating a new library, you're probably better off importing everything. You can then use MC to identify duplicates, which ones to keep, move them to a new drive (and folder structure) and delete the rest. Being able to create the necessary smartlists and observe the results will be much safer than adding import rules and hoping they work.
For your backup DVD's, copying only the tracks needed is a nice idea, but I doubt it would save any time. It would be easier and probably faster to simply copy everything to HDD prior to the above step of eliminating the duplicates. If you do that using MC, I believe it will create a separate library of the DVD's—effectively cataloguing their contents, should you want to keep them as backup.