I can answer these.
They go under /home/sdtd/engine/Mods
Each instance has a config.xml you configure the server settings in.
There may be a few ways to do this, but my personal preferred method is to use WinSCP to establish an SCP session to the Linux server and dump the files into your SSH user home folder, then SSH in as your user and copy them to the appropriate sdtd folders. Once the files are in place make sure to chown (change owner) the files.
For example if you use the
Nitrogen tool by Damocles to generate your own maps you can upload it to /home/sdtd/engine/Data/Worlds. (also try to keep your world names short or use _ between multiple words in the name as linux just likes that better and it's less confusing than having to use \ for proper formatting of hard spaces in the name.)
Code:
chown -r sdtd:sdtd /home/sdtd/engine/Data/Worlds/<World name>
Or if you copied files into /home/sdtd/engine/Mods
Code:
chown -r sdtd:sdtd /home/sdtd/engine/Mods
As stated above, chown stands for change owner. sdtd has to own all the files under the folder for things to function properly. This is especially important if your restoring files from the backup.
NOTE: I personally have a symbolic link to a separate hard drive that I have mounted as /archive. I have symbolically linked /home/sdtd/backup --> /archive/backup/sdtd.