youll set up in ahci, install windows, and then plug your hdd back in. then in bios make sure youre booting from ssd, and it should load your fresh windows install. the drive letters might be d,e or might be something else depending on what you have plugged in, youll be able to manipulate the drive letters from disk management under admin tools.
for moving stuff around / repartitioning - how big is the os partition, data partition, total? if the os partition is big enough to hold everything from the data partition, you can delete the crap on it, move everything from data to it, then delete the data partition in disk management and expand the os partition to take up the rest of the disk