Use content panes as blocks
A mini panel acts like a block, except that it has subregions.  To add content, select the mini panel for editing and select the "content" editing display.  Next pick the gear in the upper right corner of the desired region in the mini panel and select 'add content'  The pop-up will give you the selection of available content that can be placed in the panel.  

Once you have the mini panel configured, you place it in a theme region just as you would a block.  You select the mini panel from the admin/structure/blocks page for your theme.  It can be found in the list of disabled blocks at the bottom of the layout page form.