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
Manual, as well as read about some details of how to set global variables properly in the
related thread (or here is also
one from the FAQ section).
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 ;-)
