It very depends on what kind of header do you have and what are variables inside of it.
By default, you may refer to the $includeHeader
option described in one from the FAQ
When you apply miniBB to your website, the most correct approach is just to make it similar by look & feel to your website, but having its own original files. This is what you need to implement probably once and forever; but if you update your header file, it could cause new issues repeating forever.
Also, in manual you may read how to include miniBB in your own file; so there are quite a lot of approaches. Contact professionals if you don't what to do ;-)