The reason for two random number generators is to avoid OOS problems.
You use one for shared random numbers--every human player in the game must run the same code, acquiring the same next random number on each machine, to keep the sequences in-sync. If any machine fails to grab the number along with the other machines, their sequences will go OOS. This may not immediately cause an OOS error message, but it will result in some machines possibly seeing different results.
You use the second generator for cases where only one machine needs to acquire a random number: perhaps for a UI element (like the BUG "margin of error" in the vote poll which is just to be cute) or visual effect that only some players will see. This sequence should never be used for any game elements or effects.
As for seeding the first sequence when you start a game, I don't understand why you'd need to. It should continue from where it left off in the previous game. As long as Civ seeds it randomly when you start Civ itself, it should continue to produce random values no matter how many games you start.
Certainly, loading a saved game without the Re-Seed game option checked will result in the same sequence of numbers, but that should be left up to the player to decide. And starting a new game should result . . . oh, I suppose if you load game A and then immediately start a new game, then reload game A and again start a new game, you'll see the same new game with the same map, assuming all settings are the same. In that case, just restart Civ.