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Depends. If it's in Germany, you'll want to consult an employment attorney to figure out the details.
If you're working for them directly, they'll handle the details of your employment. If you're remote, they don't need to do anything except pay taxes in Germany, regardless of their incorporation location. If they want you in the states, you'll need a H1-b for long term stays, or for 60 day stints you can use the L-1 visa. Again, it's their job to sort that.
Setting up your own company would likely short change you. Ask an employment attorney about this, again.
If you do it freelance, you'll need to report the earnings and pay your own taxes, benefits, etc on whatever schedule Germany dictates for self-employment.