Keep in mind when you use the second button on the menu you will get the exact copy of the original. The problem that lies here is you are giving up quality over quantity.
I personally use only the top button with preserve menus. What this does is keeps only the movie and only the menu function of changing chapters.
If you click on all the extra options that may be on that DVD you won't get them because they are not there. I like this feature because I can change to a different chapter quickly and you don't lose too much space by using it.
What it does do is give you a better quality of the movie because it does not have to compress the files as much. Remember the single layer disk you are using can only fit 1/2 the information on it then the original, the more you remove the better the finished product.
Do a test and put a store bought DVD and use CloneDVD button 2 and see what the final compression rate is, the closer to 100 % the better. Do not burn the disk. Then keep hitting the back button until you get to the main menu. Now select the top button and do the same process. You will see a big difference, it is much closer to 100 % then the Clone selection. This will give you a better quality of the movie.
Keep in mind sound is never effected, that always remains the same.
Also on the sound streams only check AC3\6 and uncheck all the others, this will give you Doby 5.1 stereo. Sometimes disks also come in DTS Audio but that uses more space and not all stereo players can play it. By selecting both DTS and AC3\6 you are giving up much disk space that can be used for a better quality movie.
Please read the help file in CloneDVD available in the upper right hand side of the screen, it will explain many things to you.