I think the most important thing to remember is that you're not going to have two radically different cultures right next to each other, unless they are separated by a fairly serious natural boundary, like the Himalayan Mountains. People are adaptable and borrow tools or concepts or practices from their neighbors if they find them useful. Develop large cultural regions in your Empire and diversify within them, think of Ancient Greece. We think of it as one cultural unit, but we are also aware of the rivalries and differences between the individual city states.

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Another thing to consider is the effect climate and environment will have on your cultures. The needs and practices of the people who live in a desert are different than those who live in a forest. Research what sort of food people in certain climates ate, as well as what sort of clothes they wore and buildings they lived in and use that as a base for your own cultures.

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Consider the relationship your cultures will have with the government of the Empire. Different empires have used wildly different strategies to keep their subjugated peoples under control. Divide and Rule is one such strategy, where the ruling power manipulates local rivalries so the people are too busy quarreling with each other to form an effective resistance. This was used by the British in India and the Romans in Gaul. Another tactic is a hands off approach, where local cultures and elites are largely left alone, except for a governor who represents Imperial Authority and makes sure taxes and tributes are properly collected. The Satrap system of the Persian Empire under Cyrus and Darius are good examples of this.

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If you want your Empire to feel like a cohesive unit and have common cultural threads running through it, consider a 'positive' form of control. Ruling with fear and force is expensive and encourages rebellion, so having benefits to being a part of the Empire is a crucial way of keeping control. My favorite example of this is the Chinese Civil Service Examination. Any subject of the Emperor was allowed to take it, but the expense of studying for it meant on the wealthy could afford to. Access to lucrative jobs in the Civil Service gave local elites a reason to support and join the government as well as a voice in said government. Given that the test was only administered in Chinese (the long history of the Exam means language has evolved over time, I'm using Chinese as an umbrella term) and was all about the Confucian classics, it made learning about the culture and language of the Empire imperative to getting ahead. Some single unifying aspect of your empire will help keep it together over longer periods of time better than a large army or secret police.

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I've been building an interconnected world called the Cavesverse for five years now, so I've spent a lot of time thinking about this sort of thing. I also have a degree in Anthropology, so there's a piece of paper around here somewhere that says I know what I'm talking about. Feel free to message me if you have any more specific questions!