Good questions Paddy. I would personally create a folder which is dedicated entirely to the albums you create.
main HTML folder -

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- albums
In this folder I would create a new folder for everytime I generated a new album. I would then upload my new album in the folder which was just created.
This way you will have all your albums organized in a way that makes them easy to modify or delete when you are working on changes on the server.
About the file names you do not have to worry about this issue as the albums will go into each their seperate folders. However, should you want to rename the file names, you can enable the following option inside the batch operations for Photo Studio:
Should you want to name your album file names differently, which I recommend as search engine robots loves when file names are related to the content of the page, you can do this by changing the file name:
When uploading an album select the folder where the album was generated and upload the content inside this folder (incl. subfolders) to the folder you created on the server.
About the categories I would go about this using the same technique as mentioned above. However, this time I would create a category folder inside the album folder. When I have generated a new album, I would then select the appropriate category folder on my server, create a new subfolder within that folder and upload the content into that folder.
Great work on the website Paddy! I am looking forward to seeing it progress and if you need further tips just let us know
