The crux of the matter is that the program is asking users a question but they have not been given enough information to answer said question.
I assume when the program was first invisioned that it was to ease the maintenance of rom files. For all users including veterans and those new to rom files. Once it has been setup correctly I believe it does accomplish this.
I am able to use the program to get the results I want and have chosen it over Romcenter. I don't have problems with Clrmamepro once I have it setup. Although I am also comfortable performing ROM maintenance manually as well.
I agree with what was said by another poster earlier that the initial three different types of profile setup questions should automatically be taken care of behind the scenes by the program.
Whether the default action is 'Non-Merged' or 'Split', I vote for 'split' as it is more effecient.