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

Question

I have a primary domain and approximately 10 separate URL's for different clients and applications. I created a folder on the primary domain /websites/ and installed WP onto each add-on domain for each URL. Worked fine. However:

1. Is this the right installatoin methodology for this without causing problems later on? NOTE - I have considered using MU, but decided against it as I'd rather each WP instance to be managed separately (will be using WP Manager).
2. I tried to install WP on the primary domain URL, but the install was dumped into the public_html folder. I cannot work out how to put it in the /websites/ folder as it is on the root domain. This got me thinking as to whether having home/user/websites is the right path.

My goal is to set this up once, correctly from the start. Advice is appreciated.

Answer 1

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