Hm! By default C is the boot drive, there is no reason to have an os installed on a slave drive unless you expect the C (Master) to expire! And so change the drives around.
Personally I would have the larger drive as the master and the smaller drive as slave to store data.
By what you say both drives are ok but the os is just taking up space on the slave. I would delete the os from the slave as it is not required to read from the drive.
Hope this helps.