If you have installed Ghost on your own web server, then you should be able to embed a Juicebox gallery using the baseUrl method of embedding as documented here.
Essentially, you should upload your entire gallery folder (not just the contents) to your web server and paste the baseUrl embedding code into your blog entry. It does not matter where on your web server you upload your gallery folder to as long as the two paths in the embedding code (the path to the 'juicebox.js' file and the baseUrl itself) are correct.
(According to the Ghost support forum, the Ghost markdown editor accepts HTML code.)

If your blog is hosted on Ghost's own servers, then as Ghost do not offer direct access to your blog via FTP, you will need to host your gallery elsewhere (such as Dropbox) and load your gallery into an iframe, following the Web Template instructions here.