I use wordpress which has a good linking Architecture. When I go into webmaster tools, Google is only recognizing internal links to a couple of my categiries and static pages which means I am not sending page rank to the others.  Why would this be and how can I get Google to recognize the others?

The number of internal links pointing to a page is a signal
to search engines about the relative importance of that page. If an important
page does not appear in this list you should consider reviewing your internal
link structure.

An internal link allows you to link to addition area on the same web page, so it basically scrolls the page up or down to the adapted location. This is accessible to the user to bound jump to the advice he/she is searching for.