If you install any distribution in a single file system / (what you call the root system) it will contain a number of folders including the following:
/root - the home directory of the superuser;
/home - which contains the users' home directories;
/bin, /sbin, /lib - contain the system software. i.e. that which does not run in user space;
/usr - for software that does run in user space (actually, most software), contains /usr/bin, /usr/sbin, /usr/lib.
Note that the difference between bin and sbin is that the latter contains executables which only the superuser can run.
There are also /opt and /usr/local (with /usr/local/bin, /usr/local/lib) which are generally used for software from outside the distribution. For example, if you install Adobe Reader from Slackware, the executable will probably go in /usr/bin; if you download it from Adobe, then the files will probably finish up in /opt. Similarly, if you download and compile software, the makefiles usually direct the output files to /usr/local, though this can be changed.
The problem is that if you reinstall the distribution, possibly updated, all will be overwritten and any non-distribution stuff lost. However, there is a way round. If you, for example, nominate a separate partition as /home, then the original folder /home will always be empty but the designated partition will be automatically mounted on it and will contain the user files. Now, if you reinstall, you can instruct the installer to use this partition as /home but not format it and thus preserve the old user files. You can do the same with /usr/local, so that /usr/local/bin etc. will be created on the new partition, and thus preserve the non-distribution stuff; whether you do so depends on whether you are likely to have anything to preserve.
Notice that installing software in any folder under /opt or /usr requires superuser permission and is available to all users. However, user files also contain /bin and /lib; users can normally install and run software here without permission, but it is only available to the specific user.