"Scoop" is almost always associated with the "Middle" frequencies of the range. A high setting will boost your mids and a low setting will lower them. They call it "Scoop" because if you look at a line of frequency faders ( ------ ) and you lower the mids (\__/) the line looks like a scoop. This can be handy in making your guitar sound a little thinner so your vocals can fill more space in the overall mix.
The Phase button is probably associated with the pickup itself. In-phase or out of phase. This can be handy when trying to control feedback while playing live. otherwise it probably doesn't have a whole lot to do with the overall tone of the guitar... more or so just how the guitar may react with other instruments and electronic equipment around you when you're plugged in.
As for the over all EQ question... I find it easiest to dial in a very basic EQ at the amp... then control the rest from song to song from the guitar. This way you're not constantly walking over to the amp to tweak here and there. But beyond that, you should sit and tweak around with the two EQ's you might find some interesting tones that are created in relationship to each other's EQ's.