You can modify the formatting of the built-in heading styles to anything you want.

The key to having them used for numbering is to link them as described by Ms. Kelly.

The built-in headings have many advantages, such that I can't imagine not using them.

However, you can use other headings or styles in a TOC. This is described in Shauna's article on creating a Table of Contents. If you want a different approach to this you can look at:
Generating a Table of Contents - Complex Documents

And that can be handled by adding space-before formatting to the style you are using for that heading.[not header]
Understanding Styles in Microsoft Word
Sections / Headers and Footers in Microsoft Word 2007-2013

I know that I have tossed a lot of reading at you. If you truly have responsibility for maintaining a large document, doing the reading will save you time, probably as much time as you spend doing the reading within the first week.