When I started clicker training I thought it was a pretty simple and forward concept: ‘You bridge (click) the wanted behaviour and give the horse a treat. Make sure your timing is right. That’s all you need to know.’
Bridging and getting your timing right are both very important and it was an excellent start. I have been training horses with reward-based training since ’99 and I still learn so much every day. It helps that science is coming up with new discoveries, too. And that other trainers (horse owners as well as professionals) are sharing their experiences over the internet.
#1 Timing
Of course timing is important. In clicker training we say: ‘You get what you reinforce.’ So if the horse is displaying some unwanted behaviours, that means that the trainer has a question to think about: Did I bridge or rewarded this behaviour in any way or is this be self-rewarding behaviour? In self-rewarding behaviour the horse found a reward which motivates him to do it again.
The timing of the bridge (click) and the timing of giving the reward are both important. Those two moments are reinforcing the behaviour of the horse at that time. So, if you click for a wanted behaviour and your horse is doing an unwanted behaviour (pinning ears, snapping, pawing) at the moment you give the treat, you are still reinforcing something you might not want. It might not show directly, but it will show sooner or later.
#2 Emotions
You are not only training just the behaviour but there can also be an emotion attached (associated) to that certain behaviour. In the beginning I never paid conscious attention to Sholto’s emotions back then, while I clicker trained him. I didn’t notice unwanted or dangerous emotions (rage, fear, over-arousal). To be honest I don’t think my pony experienced those during clicker training. He seemed very engaged and eager to work with me if I was preparing to do some clicker training.
Looking back at my training sessions using Natural Horsemanship this aspect was less important. The horse was required to fulfill his task regardless of his emotional state.
In clicker training it is much more a two-way communication. You have to be aware of your horses emotional state because it is a part of your training. When you click you click for all aspects of your horse at that time, his physical stance and his emotional state.
My current horse, Kyra (see picture), did express a lot of fear in the beginning and I started to take her emotions into account while bridging certain behaviours. I’ve learned that you can strengthen the a certain behaviour by reinforcing that behaviour.That behaviour might be very much attached to an undesired emotion. Now I pay a lot more attention to horses emotions when I bridge a behaviour and I can use this information to my advantage.
Much more
There is much more I can tell you that I have learned over the years. I am really excited every time I discover a new use for an old tool or approach. To me my journey to the reward-based training method still is very exciting.
What was one of your eye openers on your journey?
Read here part II of New Uses for ‘Old’ Tools in Clicker Training
HippoLogic -> Clickertraining.ca 
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I didn’t think you could reinforce an emotion, emotions are involuntary whilst behaviour is voluntary.
I agree we need to be aware of the emotions as they can interfere with learning.
http://eileenanddogs.com/cant-reinforce-fear/
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