With your DiscoverEU Interrail Pass, you can benefit from discounts on different ferry lines. A few are even included (almost) entirely.
The way to book tickets for the ferry depends per route and operating company. Some can be purchased online, while others will require a booking by telephone, e-mail, or in-person at a ticket desk. It can also happen that the ferry company requests you to purchase a ticket at the full price, after which they will reimburse the discount back to your bank account.
You can find detailed information on making ferry reservations on the Interrail website. Each ferry route is highlighted here, as well as their discount rate and booking procedure.