Once you have downloaded the zipped file for either pop!site or pop!site desktop, unzip these files to the Program directory inside of your existing pop!site directory. For most people, the path to this directory will look something like this:
C:\popsite\Program\
or:
C:\Program Files\popsite\Program\
popsite.zip should contain: pt.exe, ptshell.exe, pteng.dll, ptx.exe
popsitedesktop.zip should contain: pt.exe, ptshell.exe, pteng.dll