As far as I know this is how it is supposed to be set up. I think its impossible to set up the hard drives and the cage any other way. If for nothing else it helps with cable management.
Ah, your HDDs are backwards. I would turn them around so you can hide their cables easier and make it look a little cleaner.
Are you talking about the little trays the HDDs go on?
You know what I think youre actually right maybe they would fit in the trays backwards.
I hope they fit, it is usually how they're made :D Good luck!