- Can I use an installed version on My PC and a portable version without messing up each others files?
Yes. The only exception would be if you had the sketchbook folder set to the same folder at File > Preferences > Sketchbook location. In addition to being a convenient place to save your sketches, the sketchbook folder is also where libraries are installed. As long as each installation of the IDE use a separate sketchbook folder, they will be completely independent of each other.
-Can I use the boardmanager or librarymanager in the portable version to only update the libraries and boards that are in the /portable map on the pendrive?
-When I double click a sketch on my pendrive will it automatically launch the portable IDE version?
Probably not. Sketches will be opened by the program they are associated with. That association happens during the installation of the Arduino IDE. So the sketches will be opened by the installed version of the IDE (if any). There might be a way to configure this behavior in your operating system. I know Windows 10 is especially stubborn about allowing you to do anything so seemingly simple like that.