StartOS utilizes two partitions. One system partition, and one data partition. The data partition is used for all service containers, which contains each service’s data. In this case, the Bitcoin service container will contain the blockchain data.
Granular control over container location is not currently supported. So the answer is yes, you can have the system partition on one drive, and the data partition on the other. But there is very little benefit to doing this, as the system partition is very small, and the rest of the drive will be wasted. The servers that Start9 sells, which is what StartOS is designed specifically for, have only a single drive. Both partitions are on the one drive.
If it was me, I would just use the 2TB SSD, and save the 250GB for something else.