Fill Blocks from Ctools Page Manager
If you are using Panels and Page Manager successfully (they share a common interface for many capabilities) you are well on your way to getting this together. Your question does not indicate if you are using views.  Adding its functionality to your setup in conjunction with Panels/Page Manager is important for gaining the control you need.  

First, enable View Content Panes module in the Ctools Suite.  Content panes work similarly to blocks, but are 'smarter' and handle context information passed from Panels/Page Manager.  To define a content pane in views, select the add button in views and the content pane option will be available.  You define a content pane similarly to a views block (you can learn more by viewing 'Taming the Beast'). Once defined, your content panes will show up in Panels/Panel/variant/content/add-content menu just as blocks and other content types do already.

Mini Panels are also similar to blocks plus they accept contexts from Panels/Page Manager and they have the ability to subdivide the content of a block in a specific layout. LIke panel pages, they have access to a large variety opf content types including views and view content panes. They show up in admin/structure blocks for theme layouts and in a Panels/Page-Manager variant's content tab.  If you don't need the additional layout control, you should be able to accomplish what you need using the content panes from views.  

Panels Everywhere provides a vehicle for taking control of the entire display layout, not just the content area.  I works the same as Panels for content control so really will not add anything new for your issue here.

For more on panels and mini-panels see this answer.