Can I get in trouble if I submit my own paper as a sole author while employed as a research fellow?
As @Richard Erickson said in a comment, the answer is specific to your university and your contract. Here's the steps I would take if I were in your shoes:

Firstly, read your employment contract. What you're looking for is any language about intellectual property and the results of research. In the comments you mention patents and profits from patents, but that's irrelevant here. If it is specific to patents then it doesn't apply to anything that's not a patent, such as a conference paper. Assuming your contract doesn't unambiguously say that the university owns the IP...

Secondly, go talk to your university legal department. Do not cast this as a dispute. Simply tell them that you were reading your employment contract and wanted clarification about what the university's policy around IP is. Inquire over email, or get them to send you an email confirming their position if you wish to talk in person. If they tell you that their position is that you own the IP to your work, then you're golden. If they tell you that their position is that you don't and you think that your contract doesn't support that claim...

Thirdly, consider hiring a lawyer. This can be expensive and can be a massive waste of time if you're wrong about your contract (lay people generally are, compared to lawyers). Deciding if this is a worthwhile step is a personal decision based on a lot of factors I don't know.



If your university owns the IP, you're likely stuck. Your manager is most likely the person who the university has selected to approve you publishing things, and that seems like a non-starter. If he has a boss who reads your work and is "really in charge" then it might be the boss, but whether you're likely to get anywhere going around your manager depends a lot on the social dynamic.

It's also possible that you can get him to disavow the IP, but I don't really know enough about the details of contracts to comment much on that.