The Rives disc's tones are calibrated to the analog meter, per their literature. I'm unsure if the digital will work as well, but if you have it give it a try. The analog meter is nice when adjusting sub output, for example, since you don't have to keep track of numbers but rather simply adjust the sub gain until the needle hits the target. As far as the direction to point the meter, I clamped mine into the tripod with the mic facing the direction of the speakers for each measurement. The mic is supposedly omnidirectional, so aiming it up should still work.
My experience with the rives disc proved to be interesting, but achieving truly flat resopnse in my room is futile. Unfortunately, my listening room is small and prone to all sorts of room nodes. I found that flat response in one spot would yeild quite different response, even at proximal locations within the area of the room in which I was trying to get the smoothest response. We're talkin huge differences between locations only a foot apart. I discovered that my primary listening area, and the entire room for that matter, is a extensive mosaic of nodes and nulls that can't be tamed without further measures (such as room treatments or multiple subs). The degree and severity of the nodes in my room was the biggest eye opener when using the Rives disc. Perhaps that is what you are referring to when you mention 'funky stuff' in your post. Anyway, despite the nodes and dips, I have acheived a fairly flat response througout the majority of the room. Just don't get too obsessive with the calibration and trust your ears.
