You can win the game several ways (Conquest, Space Race, Cultural, etc.) - see the Civilopedia under Game Concepts|Victory Conditions for detail. If none of these Victory Conditions are met by 2050 AD, then the game looks at your score in each age and selects the civ with the highest average score in *all* ages as the winner. So, if you meet one of the Victory Conditions, a low score would not have any impact one you.
As for how's the best way to win, that's pretty much the topic of this entire forum.