I have been getting the message - script on this page may be busy....

Looking through past threads I see that it is becase I have too much in my public_html folder.
My question is ..I need what is in that file and more ..so where should I put it? (polite answers please!!)

So that I can understand how this works (I am a complete novice at this ..so plesae bear wih me) what is the difference between
public_ftp and public_html

Be gentle with me...