SSD has no moving parts, so you can put it anywhere you want. Just move the SSD and put the new hard drive where the SSD was. Just make sure the SSD won't short anything out.
I have one of these. 2 HDDs in the trays and SSD zip tied to the top of the cage. I also cut a hole in the side panel and added a fan as there is terrible air flow and my drives were getting quite hot.