Messing with my Template

Every time I try to personalize this pages template (add a list of bookmarks, add a counter, etc.) it messes up the spacing on the page so that all my left column information doesn't appear until the bottom of the blog. That was the entire reason I switched to this template. With my old template, which had the small column on the right, all my right hand information was appearing at the bottom of the blog. I never had this problem before. Anyone else experience this?