When you read a scientific article to gain knowledge of what people have done and what they are thinking, what do you take away? Often when I was working in the lab I would specifically look for reaction conditions that might work for my experiments and ignore the introduction and discussion. However, if you read the entire article you likely will not remember exact experimental conditions once finished, rather you will hopefully leave with the idea that the article answered a question and you will take away an idea. This idea is the key message for the manuscript.
Determining the key message
Often when writing articles you will discuss what the message will be when planning the article and putting together the outline. This message will infuse the article, being proposed or hinted at in the introduction, expanded upon in the discussion and possibly explicitly stated in the concluding remarks. However, if you try to include two separate messages then you will muddy the message and it will be less impactful.
For example, if my message is that the new treatment I am discussing is efficacious and well tolerated I can easily build the article around this message. Whereas if the messages are that the treatment is efficacious and well tolerated, and also that it is extremely cost-effective compared to therapies currently on the market, then there will be two narratives running through the article aimed at different groups of people and this may cause confusion.
What to do if you want to include multiple key messages?
I would suggest that if you want to have two different messages for different audiences that you consider writing two articles. This will improve the ability of the article to reach the appropriate audience, and also allow each message to have maximum impact.