Adding a little bit to sierracircle's to help you understand..... (and using the same example names sierracircle used.)
When you log in via ftp/sftp etc, (assuming you haven't set the software to do something besides what is defaulted) you will be in your users home directory or /home/bob/
in that directory you should find a directory named the same as the site you are hosting or website.com . When you change into that directory you are now in /home/bob/website.com/
if schedule.php is in that directory the path to schedule.php would be /home/bob/website.com/schedule.php . If you have extra directories (folders) to get to schedule.php you would just include them .... perhaps /home/bob/website.com/wordpress/plugins/schedule.php
Now lets look at /usr/local/php53/bin/php /home/bob/website.com/schedule.php
what we really have there is a command to start an instance of php using its complete path (i.e /usr/local/php53/bin/php) followed by a space and an argument we are passing to that instance of php which is the php script we want to run. There are multiple versions of php on the server, so it's always best to use the full path to the version you want rather than just php (which I think will still start things off with deprecated version 5.2).
BTW on a completely unrelated topic, since I used the term ftp, I really should say for security you should have your user set to "disallow ftp" and you should always use SFTP.
I also just re-read post 3 of this thread.
A website should never run under an admin user. You should only use an admin user when you need the elevated privileges.