Vossenberg wrote:I will absolutely look in the FHS standard, since I am starting with this RPi and now it is a clean system it would be great to start following some kind of standards

Look, this RaspberryPi will be a system which is only hosting CumulusMX, right?
I also assume you are using the Raspbian Image and the user you are using a user: pi
Placing the complete CumulusMX folder into /home/pi/CumulusMX would be okay and the easiest way for you without bothering with rights etc.
On Linux, each user is having a home directory and pi's home directory would be a good place top start. Advantage: You are allowed to store,update and create files in you homedirectory.
Of course, Configuration files shoul be placed in /etc , Logfiles should be place in /var/log/ and data (variable files ) in /var but this iwll make it very complicated and also working with links might confuse you as a beginner.
Hint: copy the complete installation folder into /home/pi/CumulusMX and try to get everything running. Moving and seperating the Software and files can be done also later.
Once you can start CumulusMX without any errors and once you can access the Webpages via your Windows Webbrowser (I assume you prefer also a headless system) you can use the "Start|Stop Script" mentioned above, to get a little bit more comfort.
Vossenberg wrote: The only thing I do not know about is Jans Script, where is that the stop start script?
Let me explain it in short words.
CumulusMX on the RaspberryPi can be started and run with a GUI, double clicking etc like you did on windows.
CumulusMX can also be run on a command line without using a GUI.
Both methods need a Keyboard and monitor conected.
The 3rd and most advanced method is to connect with an SSH Session over TCP and run CumulusMX. Using this method, you need to stay connected because CumulusMX is running "interactively" In the moment you logoff with SSH, CumulusMX will stop. In this case, you can use "screen". With the Screen command, you can start CumulusMX and it will run in the background. You can login/logoff and it will still run. You don't need a Keyboard,Monitor to run CumulusMX in this so called headless mode (and of course this is less resource hungry).
My Start - Stop Script will help you to control CumulusMX. You can find an explanation here:
https://cumulus.hosiene.co.uk/viewtopic.php?f=27&t=13767
But as I already mentioned: First install CumulusMX on your RaspberryPi, configure it and check if everythign is running. In step 2, you can use the Script.
Jan