I am assuming you have a primary computer on which PWP is installed normally and a secondary computer you don't want to install PWP on, but do want to run it on.
When you create a portable install, all your current settings are copied from your primary computer, so anything new on your primary computer is preserved.
If you add or change settings on a secondary computer using a portable install and want to save them back to your primary computer, you would need to use a program such as Beyond Compare or something similar than can compare two folders and tell you what is different, which files are newer, and let you choose what to copy. The folders to compare are:
<portable install>\Settings <My Documents>\Picture Window Pro\
and
<portable install>\Settings C:\Users\<user name>\AppData\Local\Picture Window Pro
The first compare covers most of the settings. The second contains just preferences, color management and session state. Normally these do not need to be synchronized.
To synchronize two portable installs, just compare and synchronize:
<portable install 1>\Settings <portable install 2>\Settings
Do not just copy the old Settings folder to the new one as that will delete any new files placed there by the installer.