To change files or folders on a Linux server, you typically use a command line program like Putty or Tera Term. in your WHM it's called a terminal and in cPanel it's the SSH tool. All of these allow for commands to run once you're logged in.
To change file permissions recursively you would run a command like this:
chmod -R MODE DIRECTORY
MODE would be the permissions and the directory is where the changes will start. For example:
chmod -R 755 /home/username
To change file ownership recursively you would run a command like this:
chown -R <owner> <folder_1> <folder_2>
An example would be:
chown -R username /home/username
There's more options with chmod and chown, but this will get 99% of what needs to be done when using these tools.