This is why now I am fully based in Germany and closed my company in UK. It started to be a nightmare. I started the company in UK before being in Germany, I kept it will being in Germany, but as basically a "one man Ltd" the Germans started to make problems (basically behaving like I tried to wash/hide money). Also, having the company now in Germany I was able to shift more expenses on the back of the GmbH, so you get some benefits there.

This is why, the best option is to take a good accountant, you really have no "magic formula". If someone is selling you "package" for a flat fee, you are nearly sure to have problems down the line. Even in good faith, when the tax authorities start to attack you because they consider that they think that maybe you did something wrong, they can make your life a nightmare and this totally legally.

So, handle everything with care, take a good accountant/lawyer and document everything.