Your new card will be recognized for what it is! It will not be shared/integrated. You might have to disable your onboard video either in the Bios or a jumper on your Motherboard. Read your system documentation.
If I buy a stocked computer with a 64MB shared graphics card will I always be limited to 64MB graphics capability or if I buy a new card that is 126MB or 252MB and put it into the available AGP slot will it run at the new 126MB or max out at 64? Plus if it will run at the new higher speed will it still be shared/integrated?
Thanks, and please don't get too technical I may get lost. Thanks in advance.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic