With clarkwinkelmann comment I decided to do some research on adapters and try to get this, after a few hours of experimenting I have managed it, it was actually quite simple but most of the time I was looking in the wrong files.
To change the save path of the images uploaded through FoF Upload to our bucket we will have to do the following:
Step 1: From the terminal on our flarum installation
cd /vendor/fof/upload/src/Adapters/
Step 2:
nano Flysystem.php
nano -l Flysystem.php
(to list the lines of code)
Step 3: On line 84 of the Flysystem.php
file we will change this
79 protected function generateFilename(File $file)
80 {
81 $today = (new Carbon());
82
83 $file->path = sprintf(
84 '%s%s%s',
85 $today->toDateString(),
86 $this instanceof Local ? DIRECTORY_SEPARATOR : '/',
87 $today->timestamp.'-'.$today->micro.'-'.$file->base_name
88 );
89 }
'%s%s%s'
--> 'uploads/%s%s%s'
(In this example the images will be saved inside the root folder of the bucket "uploads" you can change this to your liking)
Step 4: Done! check that the uploaded images are saved in your bucket in the new folder