[P]lease remember, prostrations are supposed to be difficult and painful. Each one becomes a test of your commitment, and the more difficult they are, the more committed to your own unfolding you will be when you complete them. Also, prostrations are said to purify physical karma, the karma created by violence, stealing and sexual misconduct. So it's better to have sore knees than to be reborn in hell. Of course, a little common sense is necessary. We don't want to wind up in a wheelchair or abandon our practice because it was too gruesome.
It's up to you how diligent you are, how much suffering you're willing to take on to complete the practice. I understand that after a grueling day at work, whiny kids at home, and a fight with your spouse, the last thing you might feel you need is an hour of pain. It's not exactly why you got involved in the first place.
Also, with all the ngondro practices, you have a quality versus quantity payoff. You can try to do them perfectly, or you can try to do them quickly. The implications are obvious: if you sacrifice speed for quality, you might never finish, but if you really exert yourself to complete them as fast as possible, you might find yourself unprepared for the next practice...
The point is that both approaches work, and like other aspects of practice, some balance is necessary. It is also necessary to try it yourself. What happens to you if you push yourself? Does it raise you to a higher level of commitment, or does it burn you out? Does it open you up, or does it make you more uptight? Does an allegiance to quality become an excuse for not practicing, or do you monitor yourself to do the very best you can?
With prostrations, expect a real drama to unfold. All the issues of commitment to the Buddhist path and to commitment in general will well up completely and intensely; the inner voices "Push harder!" and "Stop!" will be screaming inside your head. I hope you listen to the right one at the right time.
Lama Bruce Newman, A Beginner's Guide to Tibetan Buddhism