You don't really have to do anything but push the button when it flashes.
It is totally automatic.
Sadly - it will flash even in zones where you have already collected all the Science - so don't get frustrated. Just push the button every time it flashes.
You can send 'data' back to the KSC via any antenna that will reach, presuming sufficient electric charge. Samples have to be returned.
When you have collected all the Science you can, regardless of whether you're in the original vehicle or not, you will get all the Science if you return any craft back to Kerbin.
Example - you fly an Apollo style mission to the Mun. While in space the button flashes and you push it to get science. You separate the lander and descend - it's carrying the Science you had on the combination craft (both craft have all the science). The lander lands and the button flashes so you get more science - this time, the lander has more than the ship in orbit. The Kerbal gets out and walks a ways - and the button flashes again. The Kerbal has all the Science from the lander, plus the new.
Return the Kerbal to the craft and both have all the Science. Go back to space and
A) dock - combined craft has all the science.
B) fail to dock, but spacewalk the Kerbal to the return craft - all 3 have all the science.
Return any of the 3 (return craft, Kerbal or lander) to Kerbin... You get ALL the science - and it's magically erased from the others.
