Here's my problem. I'm trying to make a standard input box (using &#106avascript) where you would insert a number and that number would then be sent to an array in PHP, or make it's own array. What would be the code to do this or what else should I do? (My main objective is to subtract this number from another larger number)

To do what you're asking, you would have to pass the variable to a page containing the PHP code (via a submit button with a form, for example). Or, if you want to do it dynamically without any page refreshing, you could implement AJAX.

Another way to do it dynamically would be to initialize some &#106avascript variables with the values contained in the PHP array when the page is loaded, and then you could pass the user's input into a JS function and calculate the result there. However, this implies that you know the values in the PHP array ahead of time, which you may or may not have.