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Czech employment law (Prague)

Hello everyone. I'll be arriving in Prague early this July. I'm a US citizen and am employed by a US company. I am entering the country under a normal 90-day tourist visa, and staying with my partner as he's on a long-term stay for business in CR.
Immediately upon arrivial, I will be applying for the "sloučení na partnera/rodinu" or family/partner reunification visa, with hopes for a longer stay. My current employer is happy to keep my status as an employee, and have me work remotely in Prague.
The question is about employment law and my employer's rights and legal implications for them as a small, US-based business with one employee residing in the CR. Not to mention, the long-term stay visa isn't confirmed yet!
Could someone point me in the right direction as to whether it's in my/my company's best interest to keep me in "employee" status, or perhaps it's better to become a "contractor." Any help with this, or links to legal documents or information online, would be extremely helpful. Any help that leads to proper legal information I can put in front of my employer, means I'll buy you a beer upon arrival in Prague!
Thanks very much,
Terri Burgess Protected content

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