First of all congratulations for setting up a Monero node. It’s somewhat complex, but if you’re seeing addresses, then I don’t think you’re doing anything wrong.
That the one address you see per site is a main deposit address for the site (cold storage deposit), while the deposit addresses that your users are assigned are subaddresses. This helps the adapter organize addresses. If you check the cli for subaddresses you should be able to see them.
In a multisite install, each blog is mapped to one account index. On a single-site install, you will find your addresses, under the first Monero account. The label of each Monero account is the home url of the site. So you will find the user deposit addresses as subaddresses to this account.
Most wallets should be able to send to subaddresses if they are fully compatible with Monero.