Hi there and welcome to this forum. I am sure with a bit of time you will grow to be pretty comfortable with CloneDVD2/AnyDVD.
The first point with the different %'s is due to the fact that when you select the Titles to copy, Clone is still working with all the audio tracks - when you get to the next screen, it is only taking into account what audio tracks you have selected - so the 63% is roughly what you'll get.
For you second question on naming ISO/UDF image file - that is just how CloneDVD2 works I guess - but you can also just click on DVD writer.
Thirdly, yes I guess it would just play the video titles in order with no menu's.
Fouthly, the option in AnyDVD to remove annoying adverts only works when watching the DVD - it does not matter to CloneDVD2.
Hope this helps you - and I am sure I have answered some of these questions wrong, but don't someone will correct me soon enough!!