How to install software with the protected system folder ? After unpacking an .hpkg file, various folders appear on the desktop – lib, data, var, etc. I try to move the enclosed items to where they belong, but the system folder is now read-only. How to install ?
You see right the system folders are “all” read only. This is main part of the package management system. All files are linked from hkpg files.
If you want to install anything without a hpkg package, use the non-packaged folders:
/boot/system/non-packaged or /boot/home/config/non-packaged
You don’t want/need to unpack an hpkg. You simply move it into /boot/system/packages, and its contents will all appear in their proper places. That’s sort of the point of the hpkg system! 
Why i does not write this too 
Yes if you only want to install, drop the hpkg file into the package folder at /boot/system/Packaged or /boot/home/config/packaged
http://besly.de/menu/search/archiv/sys/hpkg_terminal_eng.html
Thank you very much for the answers. I think I now understand how the package system works.
Normally, a simple double click on the HPKG opens HaikuArchive, which shows you a detailed description etc. and let’s you install the app with the click of a button. Currently this installs always into the /system hierarchy.
For a bit more information, check out the User Guide, for even more in-depth and at times quite technical info, check out the Wiki on PackageManagement.
Oh, and: Welcome KantosKan! 