Like anything in gaming (& in life!) it just takes practice. However, it is difficult to switch when you've become very accustomed to another system. I used to play Forza with a controller using automatic, but when I got my G25, I also started playing GT4 (& then Enthusia) using manual, so I never got used to automatic with the wheel on the PS2.
In F1:CE you have to deal with 7 gears - at first it's easy to get "tangled-up" in the gears when you have to downshift rapidly, but now I know, almost instinctively, what gear I should be in at any given point. One of the most fscinating parts of F1:CE is figuring out exactly how to change down through the gears at critical braking points, matching engine speed to the correct gear to maximize braking force, control & speed through the corner. One thing I have noticed is that it's very difficult to do this without hearing the cue given by the engine noise - I can't imagine playing F1:CE effectively while listening to music!
With regard to 1st gear: if, in fact, the gearing of the course circuit maps is accurate IRL, it still may not reflect what works best in F1:CE. I am finding a number of corners where I definitely still seem to be quicker shifting down to 1st, although I have discovered other corners where coasting through the corner in 2nd seems to work equally well, or possibly better, as it allows a better grip & angle through the turn.