There's no hard and fast way to lay out your AD structure; Its about what works for you with the policies you create.
First things first:
Do you have a good link connecting the two sites? Is AD replicating properly?
Next I'd look for the things you can standardise.
DFS shares mean you can have the same share path in both locations then let NTFS permissions deal with who gets access to what.
Are computer policies likely to be the same across both sites and/or departments?
What policies have you got in place on your laptop users currently? is their roaming habits likely to cause you issues?


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