The best way to run a FFmpeg encode for all videos in a folder would be with a batch process.
A batch (.bat) file gets executed when you double-click it.
The following batch command will find all mp4 files in the directory and encode them using x264 slow crf 21 and put the output video into the compressed folder.
for %%a in ("*.mp4") do ffmpeg -i "%%a" -c:v libx264 -preset slow -crf 21 "compressed\%%~na.mp4" pause
Copy the above code into a text file, edit it to your needs and then change the extension to .bat
This is a great way to process a bunch of files autonomously. Remember that if your files are not mp4 to change the *.mp4 to your file type. This could be *.mkv or *.avi