First, the saves, yes, you will be able to use your previous saves. It almost never messes them up. To make sure this rare issue does not occur, just load a previous save, then make a new save slot. That way if it borks, you can load the earlier save again. Note, this borking is extremely rare and I have never seen it repeat. What would happen is skills/quests would get reset on loading the save, but I have only seen this happen once on my game and a couple of times it was reported on the boards. It was more than likely a mod issue than anything with the game. So, load your save, check your quests and skills and if all is good, then go forward.
As for the install, it may very well just add the DLC content, or it could reinstall everything. Either way, the install is going to take about the same amount of time. If you are super paranoid, you can make a back up copy or just move your Fallout3 saves into a safe place until the install is done, then move them back. Again, I don't think this is necessary, but it is a quick click and drag to make sure.