I'm lucky. My friend Gulliver isn't afraid of the clicker. He's a dog who prefers not to be talked to too much right now. I think he's suffered a fair amount of verbal abuse which many times started sweetly, in a cajoling fashion, then escalated when the desired response from Gully didn't appear. So I try to stay quiet around him, which isn't easy for a talker like me. But the clicker. Ah, the clicker. Now there's something to which he can relate. It's never been in his life, so he has no bad associations with it. To him all it means is that a tasty little treat is on it's way. So I now have a way to praise him. A way to communicate that what he did was a good thing, because he's so extremely afraid he seems to think everything he does is wrong. He'll just lay on his blanket where it's nice and safe, thank you. That kind of response is called "Learned Helplessness". It's a lesson Gulliver learned very well.
Right now, we aren't using the clicker to change his behavior, that's something that will happen eventually. Right now, we're just using the clicker in a way that associates it with fun things. We do the things he already likes, such as being petted, or targeting on my hand, then clicking and treating. It's building a foundation for future work, when I'll have some expectations of him.
If you're working with a fearful dog, you need a way to praise them that isn't fraught with danger in the dog's mind. Maybe your voice will work. If so, count yourself very lucky, and make sure you keep your words sweet. If verbal praise won't work with your fearful dog, try a clicker. Many dogs are sound sensitive and can't take the sound a clicker makes. If your dog cringes when you click, you can try a couple of things. You can wrap the clicker in your hand, and hold it behind your back. Put it inside a sock or other fabric. You can go to karenpryor.com and buy a Clicker+, which is battery operated and makes a variety of sounds, from clicks, to pings, to warbles, in both a louder and a softer version. You can use a tongue click, or, if none of the above work, you can choose one word, many people use "excellent!" or "yes!" but it doesn't really matter, or you can use a sound - "X" or "K" are common. Load the sound or word as you would a clicker by treating the dog at the same time you're saying it, then never use the word without a treat. This is a "marker" which tells the dog it did something right at the exact moment it was performed. It's also a promise, that when he hears it, he'll get a small reward.
You also need to be aware of giving too much praise. Going over the top can work with some dogs, but not for those that are fearful. Too much enthusiasm in your voice can be as intimidating as too little. So keep your Chicken Little in mind, praise her to the skies for every little step forward, but keep it on the quiet side.