I am not sure I fully get your question, but if you have created a new flow and added it to the respective LCIA methods, then this will show up in the calculation result, provdided the process where you have added the flow is also part of your system and contributing (e.g., as you probably describe, you see the flow in the inventory result).
An easy way to check whether a flow in a process is "picked up" by an impact category is to go into the 'impact analysis' sheet of the process, and select the impact category. You should then also see your flow contributing.