I'll try and take these one at a time.
Layer Break - In the manufacturing process, blank DVDs get a light- sensitive coating that responds to the laser in your DVD RW drive. Some disks are set up so that the coating can be affected once by the laser, on the first pass. These are called Single layer disks.
Dual layer disks are coated slightly differently, and also optically slightly different, and hold twice the info of single layer disks (thus, dual layer)
To write to these dual layer disks, the first pass writes the same as a S/L disk. In order to double the size of files you can write on a D/L, the laser has to offset slightly, and burn a little deeper on the coating layer, writing the second time with the (potential) same amount of info as the first pass.
In order for other systems to know when to stop reading the first layer, and start the second, info is written to the .IFO files indicating where to stop on one side, and start the second.
This is called the layer break.
The layer break is not kept during the read process, as it isn't necessary for your HD. When you start to write the file, the burner will determine where the layer break will occur (on +R discs only) to allow all the data to be written. It is not recommended to use D/L -R discs for video, as the layer break is fixed on those at the end of side one, whether that fits the data or not (you can't split a 1 Gig. .VOB file between layers 1 and 2 - the disk won't play, or at least, only half will).
That's the shortest explanation I can give for the highly technical layer situation.
Clone vs DVD to DVD copy, it's up to you and your preferences.
Going HD to DVD on a cloned file will probably have to be cloned again (to maintain the 'exact copy' you're after), but it shouldn't make any difference to the burner...