If you choose your thoughts to be the object of meditation, then, as a result of your meditation you will have empowered them more. You will have created yourself more as a being who focuses on your thoughts. Then, during meditation or when you revert to a state of living where you are not consciously aware, where mostly you are not living with awareness, you will experience a stronger habit of living from a thought focused consciousness.
This effectively is creating a mental ‘shell’ around your inner being and is becoming a block for the flow of life force energy. Still, there is a benefit you are getting from your meditation, which is you are striving to focus on your thoughts consciously or in other words with awareness. So, you are still learning, but simultaneously creating a mental ‘shell’ and noticing the effects of this ‘shell’.
If you choose breath or the energy of love as the object of your meditation, and meditate (which is a state of focused awareness on the object of meditation), then, you will be creating more of the experience of these objects in your experience, which is a greater awareness of the life force energy within you, and a gradual awareness of where this energy is coming from, a gradual homing in to the core of your being.
Increasingly, peace will be created in your mind, even though in the beginning stages you can become aware of a large amount of thought activity in your mind. You don’t need to worry about this activity because it was already there; because as a result of your meditation you are creating greater inner clarity so that you are able to better notice what is already there. Breath is the movement of energy within you coming from deepest within you and the energy of divine love is the energy that is flowing from the deepest part of the human self into it. So focusing on one of these objects will create greater awareness of these, more of an experience of these and your mind as a result will become more peaceful, gain more clarity because the mind seeks this pure life force energy as a built-in mechanism when it isn’t experiencing it.
Now, you will feel that your glass is starting to get fuller, because you will be focusing on the energy of life instead of thoughts which dissipate this energy of life. What you focus on, you create more an experience of. Genuine meditation will take a person to the awareness of their true selves which is not the superficial level of thoughts but the all pervading, all encompassing state of formless awareness and the energy of life that is one with everything (which is another aspect of life like this formless awareness). Teachers of meditation/personal development who are not sufficiently awakened will direct you to objects such as your thoughts/imaginations/feelings, which are at superficial levels of your consciousness because this is the level they are at right now, they are only aware of these levels as their experience. It is not that focusing on these objects is wrong, we can study them to learn too, just as you are learning now, but for the goal of spiritual enlightenment, this is not sufficient.
Here is an from an enlightened teacher which teaches the practice of meditation with an awareness of these deepest aspects of ourselves (*). Studying and practicing according to these guidelines therefore will facilitate awakening to these deepest aspects which will simultaneously teach you how to resolve the empty glass feeling as well. The most important factor here is understanding the guidelines and actually practicing them. Such correct (by the guidelines) practice will effectively give the experience of these states, and understanding of what has been explained in this answer will naturally develop as a result.
* (It clearly explains the state of focused awareness, how to practice, how to approach the arising of thoughts/emotions/sensations, the objects of meditation, posture etc.)