I'm not sure if this is encouragement or not, but it took me at least a month or two to start reliably placing stuff and understand all the quirks in the machine and SW. The manual has some good information in there, but I learned everything useful from the wiki and trial and error. Unfortunately I'm in the middle of moving and haven't touched the (disassembled) PnP in about 2 months so I can't fire up the SW to help.
After ou modify the parts like, say, changing the rotation ... are you pressing "ENTER" in the box that you modified the values for? If you don't press enter on the row it won't persist that changed data.