I agree with Chris, now the category of Restaurant Managers,Chef and Retail Managers is more under observation due to too many people who applied for residence in the past being just assistant or not really skilled. In a restaurant the only manager who can gain residence is the Restaurant General Manager,the one in charge of the whole operations in the establishment.
I also suggest you to look for advice of a immigration adviser, explain everything to him/her and he/she can tell you the best way to proceed, you have to explain to your CO properly that you are the main manager and your boss doesn't take too many decisions,otherwise they can decline your application.