Fill Blocks from Ctools Page Manager I am using Panels 3 and Ctools to structure my pages and pass arguments both via context as well as inputs on pane settings (fixed text as well as keyword substitutions).  The "input on pane settings" is very important to me.

I need to fill some block regions from the theme, and if possible I would like to do this via the page manager in order to keep selections and variants in one place.  

I am aware of mini-panels and that they can be placed in blocks.  But they would require to replicate all selection and context logic from the ctools page manager. 

Panels Everywhere seems to go quite deep and I cannot predict whether it will actually allow me to modify the existing non-PE theme within a reasonable time.

Alternatively, I was thinking of modifying the theme's CSS and adding css-classes in page manager or to use javascript to replace the blocks with regular panes.  Unfortunately, this would require separate variants per theme.

Are there any suggested ways to fill blocks from the page manager?  I am using D6, but suggestions for D7 are good as well.

Clarification:
I am looking for ways for filling a themes' block regions (eg. sidebars, headers etc.) from the page manager, in contrast to eg. mini-panels added and configured on the blocks screen.  I am now trying to backport bricks, but ideally the block content should be defined within 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.