Welcome to Subsim.
There are 2 ways to accomplish this.
First, load a new campaign patrol, choosing the emblem & sub type you want. Then immediately exit to base and go straight into MP, choosing the same sub. You will have the emblem you chose.
Second, paint/attach the emblem directly to the U-Boats skin (TGA). Now, if this is done with the textures only then MP won't have a problem with it.
Unfortunatetly, none of your MP friends will see the emblems whichever way you do it. They will only see what they have running on thier system.