You can make reservations on a range of sites and stations. They are independent of your pass and valid from whichever supplier you choose. As a general piece of advice always consider the alternatives to the Interrail service first - they are often easier to use and offer lower fees - Interrail charge 2 euro per seat, many others charge a lower fee.

There is no issue buying your reservation for Thalys from the B-Europe site.

Because I do not entirely understand if you need to book your seat reservation 90 days before or after? 

As soon as possible. Not all seats are available por people with a pass.

If you travel Brussel-Antwerp-Rotterdam-Amsterdam you can take the hourly Intercity trains on this route, they need some more time, but no reservation needed.

Trains with mandatory reservations have variable advance periods when they are released for sale.  Many are not released until about 90 days before departure but normally there is no fixed date. Eurostar is different in that it releases seats for pass users 180 days ahead.

Some routings have limited capacity (e.g. Thalys, Eurostar, sleepers and cross border TGVs) and these should be reserved as soon as your plans are confirmed and they are available. Many others can be left until nearer the time of travel, for example Italian Freccia (High Speed) trains where there are many services between main cities. All trains with optional reservations allow standing so you can always board without a reservation, but these are all low cost (Typically 5 to 10 euros per seat) and advised for peak times and holiday periods.