Will you please post an active link starting with http:// to the blog in question?
Every time we change themes the existing widgets we are using migrate into the Inactive Widgets box. The new theme will have a sidebar display that does not contain actual widgets. All we do is go here > Appearance > Widgets and drag install the widgets we want from the Inactive Widgets box.
The reason your sidebar has fallen and is displaying below your posts is typically caused by an open HTML tag in one of your posts which is usually a result of due to copying and pasting.
Go to Settings > Writing and select “ ___ WordPress should correct invalidly nested XHTML automatically” and then scroll down and click “Save Changes.”
Now, starting with your latest post, open it in the editor, make one minor change such as adding a space and then deleting it, and then click “Update Post.” Check your blog and see if it is back to normal.
If you have been copying and pasting text from elsewhere without using either icon 5 or icon 6 in Row 2 of the visual editor, please see here so you know how to do this correctly in the future. http://en.support.wordpress.com/visual-editor/#pasting-text