I can respont to the first two questions:1) Yes, there will be borders, and they will be visible unlike in CtP. If you cross the border into foreign territory, your opponent may complain.
But he also will most likely respect your borders. Other than in CtP or Civ2, you now can see where you can go with your units without offending your enemies up front.
2) How to manage... well, whenever you build a city you gain land, and the city mayor will assign workers on the land. It won't be a predefined area like in Civ2 (or CtP for that) but it depends on your choice of concentration in the city. (gold, science, ...)
Look at Alpha Centauri, and you will get a very good idea about the borders.
Asking what product would be better: Civ3 or CtP2, well, I don't know. What I do know is that Civ3 won't be ready for at least a year, while CtP2 will be released very shortly (if they don't delay it!)