Stay away from RailEurope which is just a ticket reseller that doesn't even show you the complete listing of available trains. They are worthless.
Yes, of course there is a place to enter your Swiss Saver Pass informaton. After you click the "buy" button to purchase your specific train journey the next screen says:
"Reduction for
(only reductions the passenger is already entitled to) "
choose one of the entries from the dropdown:
GA 1.cl, 1 year /GA subscription
GA 2.cl, 1 year /GA subscription
depending on if you are traveling 1st class (GA 1.cl) or 2nd class (GA 2.cl)