is it too late for me to do my overrides properly?

I know there is lots of info about how to recover from hacks but I have an extra problem:

When I set up my site I didn't do the over rides or rename any of my files. It was only later that I found out I should've done this. So all my files are the original names and I read somewhere that this could be problematic when downloading updates.

My site was hacked recently and although I want to sort this out I don't really know enough about how Zen Cart works to do this. Because I didn't use the over rides system I'm worried that any changes I make and patches that I download will not work or indeed ruin the whole site.

So I guess my first question is, is it too late for me to rename my files as I should've done at the beginning and if not how do I go about this? Even basic stuff such as where files are stored are quite confusing to me so please treat me like an idiot with any advice.

I hope I've explained the problem properly. Thanks for any help.

The Tutorials/FAQ link at top of this page is a good place to start learning.

As to your current overrides problem, presuming you've been customizing files in directories called 'classic', you need only change them to whatever you want to call your Template. No need to change the files inside.

Note: you will have to re-upload the 'classic' directories you rename as they do need to be there.

If you've been editing your files locally (on your PC/MAC) and uploading them to your site, you might be able to identify the files you've changed by the dates and move only those files over to your custom folders.

Read my technique here:

http://www.zen-cart.com/forum/showthread.php?t=135481