A Juicebox gallery is essentially just a <div> container, and it will appear on your web page at the dimensions you give (via the galleryWidth and galleryHeight options in the embedding code) and wherever you put the <div id="juicebox-container"></div> in your web page's code.
It sounds like you might be trying to embed a gallery into a page with a complex layout and the gallery dimensions you are currently using might not be suitable for your page layout.
If you are not already doing so, try using a galleryWidth of 100% (so that the gallery fills its parent container's width) and a fixed galleryHeight such as 600px. (When using a percentage height, you would need to make sure that the gallery's parent container has a height set via CSS, otherwise Juicebox may not be able to determine what its actual height should be a percentage of.)
If this does not help, then please post back with the URL to your gallery's web page so that I can take a look at the problem for myself and hopefully help further. (It sounds like you may need to either move your <div id="juicebox-container"></div> container to a different location in your web page or change your gallery's dimensions.)
Well you can't include the Juicebox created "index.html" file due to the existing "index.html" file that's already a part of your page, correct?
If you already have a file named 'index.html', then you'll need to take care not to overwrite it with the gallery's own 'index.html' file.
There are 3 options:
(1) Rename the gallery's 'index.html' file before you upload it to your web server (to ensure there are no duplicate filename collisions).
(2) Delete the gallery's 'index.html' file. This file is required only if you want to display the gallery on a web page of its own. If you are embedding your gallery into an existing web page alongside other content, then the gallery's own 'index.html' file is redundant and can safely be deleted.
(3) Use the baseUrl method of embedding documented here. This allows you to upload the entire gallery folder (not just the contents) to your web server so there will be no chance that the gallery's 'index.html' file will overwrite any similarly named files that already exist on your server.