It takes some practice to get into the clutch. I have driven standards for almost 12 years now, and it still took me a little longer to get used to the clutch. It's one of the few things my wife does not like about the car. Now that I'm used to it, I don't notice the clutch/gears at all. Practice makes perfect.
The only problem being now that I tend to drive my wife's car kinda funny....