Looks like a good start on a template.
The effect you mention is due to the sideboxes all having a margin-top. This spaces them down from the previous sidebox, and also spaces the top sideboxes down from the header. If you want the sideboxes up against the header, you could either remove the margin-top on the two sideboxes, or change all sideboxes from margin-top to margin-bottom.
Code:
#categories, #search {margin-top: 0;}
.leftBoxContainer, .rightBoxContainer {
margin-top: 1.5em; <-delete
margin-bottom: 1.5em <-add
Bookmarks