Each person would develop their own way of using the interface
Each person's brain develops differently. That is one of the joys of humanity. However, we have to interact with each other, so clearly we need to develop a common ground. We develop language for this. However language is not fixed in stone, and that is what I base my answer around.
The closer one gets to the "core" of an individual, the more customized and fluid language becomes. This is because, as you get closer to an individual, you relate to them more, and have more common ground to work from. Consider how you would ask someone to take out the trash for you, given different relationships:
- Stranger: Hey, how are you doing? Look, can you do me a HUGE favor? I'm running really late for a big meeting at our city hall, and I forgot to take the trash out. If I don't get the trash out, my wife will kill him. You're married right? You understand? Do you think you could help me out and take the trash out? Thank you!
- Friend: Blast! I forgot the trash today. Do you think you could take it out for me? I'd owe you big time!
- Close Friend: Hey, think you could take the trash out for me?
- My Wife: Before I can possibly forget the trash, she throws just one glance at me, to remind me that I need to take the trash out right away. This glance is different from the "time to clean the catbox" glance and very different from the "take the trash out at halftime" glance. I wonder if I can pretend I saw the halftime glance instead. Nope, she saw my glance, and responded with another one... that glance was mean... I better take it out real quick, and buy her flowers tomorrow. Yep, that glance says its a good plan.
It is reasonable to extend this to how we handle our muscles. We develop a decidedly personal language with which to express what we want the muscles of our body to do. It is part of why personal training after an injury is so hard: our muscles and nerves are no longer speaking the same language they used to. We have to develop a new language.
It is also worth noting that we speak the language of our body so fluently, and there are so few misinterpretations, that we often even forget that it is reasonable to model our mind-body interactions this way. We usually get surprised when someone does something to our body to disrupt this communication (like nerve pinches).
Accordingly, each and every neural implant owner will develop their own personalized way of interacting. However, there will be standard ways of learning.
An infant learns to handle its muscles the hard way: trial and error. A child learns to speak their native tongue the hard way: trial and error. However, when learning a second language, whether its a second spoken language, or a different way to handle muscles (say, how to swing a hammer), the rules change. We can start by describing what we want to do in our native tongue, then slowly translating that into the second language. At some point, we find we are no longer translating... we have indeed learned a new language.
This occurs with people learning martial arts, or yoga all the time. They try to do the forms using the body-language they know, until one day someone shows them there is a new muscle that they'd had the entire time and never used it to its full potential. At that time, the practitioner has to begin learning a new language!
How can we adapt this to neural interfaces? If the neural interface is implanted from birth, we will learn to use it intuitively, like a muscle. Calling someone will not have an image, it will simply be a decision to call someone with exactly the same flair as the decision to pick up a glass of water.
If the neural interface is implanted later, we have to learn to use it. This could be done in the infant style, but it isn't as efficient. We're smarter than that. What companies will do instead is provide common visuals for calling. They might be visual or auditory. They might even be the physical act of mimicking picking up a phone. Anything which allows the brain to have the control needed to make a call is sufficient.
After that, the plasticity of the brain will take over, hopefully aided by a plastic neural interface. The brain will begin developing a new language to communicate, exactly how we transition from total strangers, to friends, and for some, husband and wife. Someone whose initial interface calls for visualizing the phone number or IP address of a person to make a call, will watch it shift to something more organic: perhaps the name of the individual. Eventually it will be the face of the individual. Eventually they will just think about calling the individual, and the neural link will respond.
There will be an interesting phase where it gets hard to explain the visualization you are using. Someone may claim "I picture their face, and it calls for me," but when faced with the puzzler, "if you pictured someone's face right now, without wanting to call them, would it call anyways?" the answer would be a very frustrated "no, it wouldn't, but I have no idea why... it just wouldn't. It knows better." The visual would be only part of the communication... the rest would be in the tiny subtleties the brain develops (the equivalent of the married couple's glance communication).
Note: The more complicated the interface (your 3 element system is nice and simple), the more complicated the training would need to be to gain control quickly. For something very difficult, like a neural link to control a powered exoskeleton, there might actually be schools to teach you how to learn to talk with the implant (similar to physical training classes to teach you to use your muscles again).
Note: such neural interfaces would likely aim to be as plastic as the brain, because its much faster to develop a language between two plastic things than it is to develop it all on the brain side. This has huge positive implications when talking about dealing with viruses and other highly negative aspects of neural interfaces in science fiction.