I've been really confused with this topic, but I need to know how to launch FOSE with Steam. I also need some questions answered, Will it use the original Fallout 3 game tab (Where you select it in your Library) and if so, will it still track my play time?

I simply start Fallout 3 by clicking fose_loader.exe. It works great for me. But I play all of my Steam games in Offline Mode. I've never once tried to play online, so it's possible that this may not work for you.