For the site structure, you will be far better of following the PDF Instructions. Some of the files in the WA Specific folders will be unique to powerCSM. Same for the WA_Globals file, the WA_Globals file for one solution pack is not the same as the WA_Globals file for another solution pack.
You will save a lot of hassle and digging to find what is what if you upload all of the PowerCMS files into a subfolder.