I am very novice at html and even more so with java, but I have found what I am looking for. I am using this drop-in template, Kil'Jaeden, and looking to change the menu buttons. I have found in the showhide.js where it point to the gifs. I have the program to edit the js and point to a different link with different buttons, but how do I, if I can, upload the edited showhide.js?
You'll want to upload the file to the Administrative File Uploader, which will give you a path for the newly uploaded file.
Then, when it's uploaded, you'll want to head to Admin > Layout > Advanced Layout Options and download the current layout file. On that page, you'll see the reference to the current showhide.js file. Change the path to the newly uploaded file, then re-upload the layout file to that page and click "test It" to see the effects in action.