"Each" vs. "both"

Solution 1:

The meaning of the sentence changes completely if you use each vs. both:

If you say: "Both the datasets ... are stored in two schemas." then you are saying that there is a total of two schemas. (but we don't know how the datasets are divided between the two schemas (50/50? 60/40? 90/10?))

If you say: "Each of the datasets ... is stored in two schemas." then you are saying that there is a total of four schemas: two for one dataset, and two for the other.

If you want to say that there are two schemas, and that one schema contains 100% of one dataset, and the other schema contains 100% of the other dataset, then you should say: "Each of the datasets ... is stored in a schema", or "Each of the datasets ... is stored in its own schema."

Both should only be used when you want to refer to the combination (sum) of two things: The car and driver both weigh 3,510 lbs. (If they each weighed 3,510 lbs, the driver would need to go on a diet)

Solution 2:

Both options that you are considering are unclear. In other words, each of the two is unclear. To be perfectly clear, say:

The datasets HapMap 6 and CEU HapMap 610 are each stored in an individual schema.

or

The datasets HapMap 6 and CEU HapMap 610 are stored in two separate schemas.

And then,

As far as are vs is, I think is goes with each because each is singular. Both is plural, so that should go with are. Is that correct?

Yes.

On a side note, is there any reason to prefer the datasets HapMap 6 and CEU HapMap 610 to the HapMap 6 and CEU HapMap 610 datasets?

No.