Inserting Google Adsense Advice

I know Google is always changing something, last time I let Google put the ads on my site automatically it screwed up my pages. The funny thing is I only had a very simple straight down the page design. I found the only way to get them to fit and display properly, was to manually insert them in a column with the custom code tool. I’m I doing something wrong? Has anyone else had issues with adding ads automatically?