the difference in day to day usage is minimal.
can only be seen on benchmark softwares.
but if you're working with very big files, the transfer rates with the NCQ enable is noticeable.

you should be able to see the slight different in transfer rates.

yes, you can. but only the hd with NCQ feature will benefit most.

i suggest you keep the windows in the smaller drive intact and run full installation from the bigger drive; if you really wanted to experience it yourself.
if anything goes wrong, you can always disable the ahci and boot as usual from the smaller drive.
btw, you should use the smaller drive as a master where the OS is installed and the bigger drive as storage.
raid wasn't a favourable option, unless you're into video editing or web servers.