As easy as FP makes it, its actually better to just use FP to make your pages, then upload using whatever FTP program. I find you have a better control over everything that way.
In a nutshell you will have to maintain the entire site with FP in order for everything to work, so each folder or directory you make locally will then be uploaded to your server as part of your main site... the alternative is to make each gallery a new site - way too much work in my opinion.
Simply put. Find yourself an FTP program, like FileZilla for example and upload this way.
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