The new cylinder head gasket for my dt250a appears to have an "UP/DOWN" orientation to it. I see no mention of it anywhere in the service manual. Which side faces "UP" if anyone knows or if it even matters? Thanks.

Ridge Up.

LOL, this is not in the Yamaha manual I know of. A similar setup is we used to O-RING V8 engine heads to keep from blowing gaskets under extreme boost and detonation. Want to say was a 0.030" grove. Would do this by milling out a grove in the head for an o-ring type gasket to seat in, then put slightly less torque on exhaust heads bolts so when and if she blew, went out the lower side.

In the case of the Yamaha, I'm thinking it must form a firewall to keep combustion from escaping.

Hope that helps. BTW, this is my opinion on the matter. I have not read this in Yamaha docs.
Reminds me also, I reused a few gaskets.  i guess if you turn them, you get a fresh side.  haha.