If you only have changes to the core then you can just use
yourfile_name.ocmod.xml
If you want to (also) add new files, use the upload folder as you've found out. If you only want to add new files I guess you can have an empty install.xml (with default tags for author,version etc)
iow install.xml is the former vqmod xml but with ocmod syntax (position to 'add' tag, index starts at 0, less robust search)
I use install.php for adding db tables, layouts, admin permissions and so on. I'm not sure if install.sql is useful as the db prefix is unknown
If you have an installable module(from extension page) the install() function can also act as install.php
Hope this helps

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Thanks!