I haven't put the covers back on. I did my wife's 53 reg focus about 4 years ago and I know the car is still driving about without the bottom cover.
I did the wifes 10 plate focus about 2 months ago and thats still ok.
I also tried the car with it in gear and someone with there foot on the brake and it didnt work.
I thought it qas alot easier to time the engine up this way too cause you can turn the crank over whilst the time cam pulleys can spin.