You can also use the --profile
switch to point to a new location but that isn't an officially supported method and could lead to issues.
Worth noting that if you use that or @joeldebruijn's joplin portable suggestion you can still only run one instance of the application at once.
One other potential solution is one I have been using until nested/hierarchical tags are introduced is to prefix your tags with the "section" they are in then render the first character invisible with CSS.
I should also note that I use a bit of a hack to organise my tags in lieu of having a proper hierarchy so that the various categories aren't just jumbled up together.
I basically have an extra letter at the start of each tag to "categorise" them, e.g. book related tags might be called something likebCookbooks
andbComicbook
whereas I might have some recipe related data that is stored underrChicken
orrAubergine
. I then use the CSS hack I posted about here - Share your CSS - #296 by Daeraxa - to hide the first letter of the tag.