What is the best method of installing WP on multiple add-on domains?

You can install WordPress wherever you want, stick it in the directory and run the setup.

We have a sites.ourcompany.com/client-name setup that works excellently. If you want WordPress on the root domain, public_html should be the appropriate directory for it, unless you want it on /websites/ at which point you can just drag WordPress into that directory and run the installer there.

So for your first point, this methodology is totally fine. It gets cumbersome with a bunch of sites, but that’s where the benefits of a WP Manager set up comes in (such as iThemes Sync, WP Manager, Manage WP, WPMU’s “The Hub”, etc.)

For your second point, I’m not entirely sure what you’re asking since public_html is the defacto “I want WP on my domain” folder, and if you want it in a subdirectory, just install it in a subdirectory

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