That's an interesting question. I have also often thought about what tangible transformation or change we can see in ourselves when relying upon a Dharma protector practice.
In thought: I think the nature of a Dharma protector is to remove obstacles to our practices, both inner and outer. So he helps us to receive the necessary outward conditions and remove inner doubts, negative patterns of thinking so that we gain more faith in the teachers and a stronger understanding of the teachings. I think this is one of the most powerful ways a Dharmapala helps us. We could have all the most perfect outward conditions to practice, but the one thing that will stop us from doing anything about it is our own inner demons - our laziness or doubt or attachments. The Dharmapala helps to release us of these inner blockages so we become more open to practice, learning and application.
In deed... This automatically leads on if we rely on Dorje Shugden in thought. Once our thoughts and ways of thinking change, our actions will naturally change too. We find ways of helping others, we become more resourceful or more caring, we change our actions and outward behaviour to suit another person and to help them. This results in two things: we are physically and directly able to help someone in a more capable manner, with clearer thinking. And at the same time, by our own change in actions, we inspire other people who will look upon us and feel encouraged to practice or change themselves. So we help them directly and indirectly to bring transformation to their own lives.
What is important to realise is that reliance isn't about just following or relying on something blindly, but understanding the benefit that can arise out of it. You may not understand it in the beginning, but there is also some degree of having faith in your teachers (it begins with the teacher-student relationship) and understanding that a teacher would not give you a practice that would harm you. As you do the practices, you collect more merit and purify and your mind becomes sharper so you can understand. So you switch from just merely following an instruction to developing your own relationship and connection with the yidams and protectors.