If you create the TOC using Insert | Reference | Index and Tables, even if
you accept all the default settings, you should have a functional TOC with
numbering where it should be. There are many things you can do to spiff up
or customize the TOC, but aligning the numbering should not be an issue
*unless* you change the margins after inserting the TOC. When you first
insert the TOC, Word sets a right-aligned tab stop for the numbers
dynamically based on your current margins. That tab stop doesn't change if
you later change the margins, and you will have to adjust it manually (using
Format | Tabs or by dragging it on the ruler).

For help with TOC basics, see
http://www.ShaunaKelly.com/word/toc/CreateATOC.html. For more advanced
techniques, you can see http://sbarnhill.mvps.org/WordFAQs/TOCTips.htm, but
not until mvps.org comes back online (it's currently down).