The first thing Atem did upon realizing he had his own body was hold Yugi for the longest time. Yugi seemed confused, but let him hug him anyway.
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Yugi gradually accepted that his Yami was no longer see-through. He eventually became accustomed to Atem's warm hand that often wandered to the small of his back or to lightly touch his own hand. It became a fact of life, much like the fact that he had another person inside him just a few months before.
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Soon, Atem became pretty familiar with the modern world. Yugi no longer had to walk him through things, except on a few occasions. Yugi hardly minded, but he found himself relieved when Atem learned how to properly use the oven.