Hello Tryerina and welcome to our forum,
the page you linked is in German so I assume you know German as well. We got some staff members of our office in Germany lurking around in these forums (e.g. me) so feel free to ask your question in German.
The Skylake generation of CPUs has a fairly low thermal design power and should be fine (especially with a 160mm tall CPU cooler). A GTX 980 can develop a little more heat so primarily you should worry about keeping your VGA cool.
The traditional recommended cooling setup sucks in air from the front and/or bottom and/or side and blows it out at the rear and/or top. It makes sense to adjust the CPU cooler to the direction of the airflow (sucks air from the front, blows it out to the rear).
How important is noise to you? Please bear in mind that taking out one of the dampening panels at the top or side will increase the noise your system makes by a little, while it benefits the cooling capabilities. Upgrading the cooling without removing any sound dampening panels is only possible by adding another intake fan at the bottom.
Taking out the HDD cages is a good idea as it allows the 200mm front fan to do a lot of work. The default fan design of the F51 is actually already quite good with 1x 200mm and 1x 140mm fan. I would suggest to first build the system and use a tool like "CPU-Z" to measure the CPU and VGA temperatures under a bit of load. If the VGA gets too hot, you can think about installing an intake fan in the side panel, which delivers fresh and cool air directly onto the VGA.
For reference: According to NVIDIA, the GTX980 can endure up to 98°C. This is obviously not recommended. A good rule of thumb would be that anything below 80°C at full load is fine.