You may consider using subdomains, such as store.example.com and blog.example.com. A challenge to using subdirectories as you listed is that the One-Click Installs (automatic application installer) usually require an empty directory. This means that you must either install your main site first, or manually install it later.
To create a site, or sub-site, you must first set up a Fully Hosted Domain from the panel: Domains -> Manage Domains. This will create an example.com folder in your FTP directory, and that is where you files go. There is no public_html directory here.
I don't like to think of DreamHost as being "complicated." I find it to be "flexible." I really like the control it gives me and cPanel has been washed from my mind.
Post back if you have any more questions.