I believe it is best to maintain the visualization continually while you practice. To do this, you will need to memorize the prayers and be able to recite by heart.
As you are reciting/accumulating Semkyed, you are seeing the compassionate eyes of the deities on you and all sentient beings. At the same time, you are generating warm-hearted compassion to all sentient beings. But the visualization is maintained the whole time.
Similarly, while reciting/accumulating Kyabdro, you maintain the visualization of the deities. You feel their presence and feel connected to them. You give them your complete trust and feel that you are under their protection.
It can be challenging to recite the prayers, generate the feelings of compassion or refuge, and maintain the visualization, all at once. It might be helpful to break it up at first, by just memorizing the prayers, or just visualizing while generating the states of mind. It is absolutely ok to begin in a simpler way. But in the end, it is best if you can bring it all together and maintain the visualization of the deities as you recite the prayers and generate the desired states of mind.