Upvote:0
You can use different documents for different purposes. I have two passports/nationalities. How do I use them when I travel? has some info on how you might go about it in general. If there is any confusion, you can also simply present both and explain your situation.
The most important point is that it doesn't matter as much as many people seem to think. You have a right to work in Germany based on your citizenship, not the document you present at the border. There is no way you can be deemed to be working illegally in Germany, be forced to leave or lose your right to stay and work in the country because, say, you used the British passport to enter.
Upvote:1
You can travel in both directions using both passports. In most cases crossing a border involves two separate steps: you go through exit control in the departing country and through entry control in the arriving country.
So you use your UK passport when you go through exit control in England and use your EU passport when you enter Germany (or any other Schengen country).
As a general rule: