I wrote it for $content on a page, but I've used a similar technique to break up the side bars into smaller segments.
How?
In PHPTemplate, the $content variable passed to page.tpl.php is constructed by passing in nodes to node.tpl.php and then concatenating the results.
The $sidebar_left and $sidebar_right variables are constructed by passing blocks to block.tpl.php and then concatenating those results.
Therefore, if you insert a delimiter (I use HTML comments: <!-- DELIMITER -->) into either node.tpl.php or block.tpl.php you can find it later and break up the $content, $sidebar_left, and $sidebar_right variables using
$an_array = explode($delimiter, $the_variable_tosplit)
As an example, I've used this to create "tables" of blocks using only CSS. I float all the blocks left using CSS, and after every third block I insert a <div> that clears the blocks. The result is an 3 by n table of blocks (where n = total blocks / 3).
I'll create another snippet to show how this works. I don't think I'll have time today, but I'll see what I can do tomorrow.
For what it is worth, I don't think this addresses you earlier request, but I thought I'd post it anyway as I think it is an interesting technique.
-M