Make sure you've got HTML comments enabled (it is by default). View source of one of your pages and see if you can find:
The above indicates the start of the headerinclude template (obviously).
I'm not sure what you mean by 'creating template prefix', since you don't create one, but assign one. Maybe I'm just being pedantic with terminology here, but I'm not sure exactly where you're looking at.
I'll try to explain what the template prefix does exactly, if it's confusing you. Basically, it's to allow you to use different templates in different forums (in other words, have unique templates for some forums). To do this, we need some way to separate normal templates with ones we only want to apply for a specific forum - this is done by assigning a unique prefix to the name of the template.
So if forum X has a prefix of "cr_", when MyBB tries to load the showthread template, it will first look to see if it can find cr_showthread, and if not found, will fall back to showthread. Note that cr_showthread effectively replaces showthread in this case.