Yes regarding the transparencies, that is the way Poser works. You only get to see the effect upon rendering at which time the image may be saved. A tip to aid in the composition of scenes containing semi transparent objects is to set their display mode to cartoon. (Display/Element Style/Cartoon). In this way you can see what you are doing better.
As for the clothing, can you give an example. There are several types of clothing and a general answer at this point may lead to confusion.
Morph targets may be added to clothing. One way is to use the magnets. This is a whole topic on its own and a full answer would fill a book. My best advice if you are just starting is to give it a go, then holla and we will come and pull you out of the mire :)
Good luck