You can book seats for multiple people in one transaction, so you'll be seated together:

https://www.eurail.com/en/help/reservations/how-do-i-make-seat-reservations-together

However, first check this page to find the best places to book reservations:

https://seat61.com/interrail-and-eurail-reservations.htm

I want to ask if I have two passes, each bound to a different phone.

Can I separately link these two passes when booking seats through the website,

assigning one to A and the other to B? Or can I link both passes to my A journey?

Hi @Jing Ya 
 

The seat reservations done through our website do not synchronise with the App, this means that you can create a separate trip on the website for making reservations. On the App, you would need a separate trip for each passenger if you are travelling together and you want to have both Passes on your phone. At the moment of inspection on the train, you need to show the QR code generated on your App plus the reservations done through our website. It may appear difficult, but trust me, you will get a glimpse of it pretty soon.

Let us know if you have further questions. 

Have a nice day!