"But I'm noticing other weird things, for example there is no Question "Which morphs do you want to keep?" or which morphs you want to transfer. Instead i just get a window with a list of morphs. "

So you selected the check boxes and then during the conversion process you were presented with the lists from which you make your selection? I'm not quite sure I understand your problem. You expected to be presented with a list immediately you selected the checkbox?

"Also when analyzing, i get a list. and I'm not sure if i have to select them or not . when i click on them they get a bit highlighted...."

It is a standard list select box. Left mouse button to select one. Command+click to select several, Shift+click to select a block. Your selected items get highlighted, I believe on mouse over the item gets underlined to help you identify exactly which item you are over.