If you install Flames of Vengeance after the PC version of D2:ED, you can continue with your original saves, though some of the changes made in DKS (redesigned flying fortresses, changes to enchantments, enemy placement, loot, etc) will not be applied (some engine and graphics updates will). After you finish your current character, there is a patch to convert D2:ED + FoV to DKS, if you want to start a new character to check out the changes in the remastered version.
So if I get FOV does it include the expansion,loot,quests...ect ? Or do I need to get both in order to get the full experience