Hi. Ideally, you'd be doing some bass management to send separate frequencies to the sub versus the speakers. The Marantz can't do that, but your sub might be able to...depending on which version of the plate amp you got. Does your sub have "HPF OUT" jacks next to the "LINE IN" jacks?
(*) If your sub has HPF OUT jacks, I'd suggest running the two PRE OUT jacks from the Marantz to the sub, then run cables from the HPF OUT jacks on the sub to the inputs on the amp
(*) If your sub does not have HPF OUT (or LINE OUT) jacks on it, then you can simply get two RCA y-splitters and run cables to both the sub (like you do now) and to the amp. The end result would be (I think) no different than how you have it now in regards to bass management, except that you'd be using the external amp to power your speakers