Actually what you're wanting to do is very much easier than what is done in BootstrapBase/Clean. The way it is in those themes currently with nesting etc. will probably only confuse you. Since you're doing something so much more bootstrappy, rather than Moodley, starting from the Bootstrap docs (http://twitter.github.io/bootstrap/scaffolding.html#gridSystem and search for "fluid grids") is probably easier.
You only need a single row and the three columns would be:
<div class="row-fluid">
<div class="span6">Main</div>
<div class="span3">Pre</div>
<div class="span3">Post</div>
</div>
If you want the block columns to appear and disappear and the main content to vary its width in response then you need to increase the span of the Main section to compensate so it still adds up to 12, depending on how many columns are present in the content:
<div class="row-fluid">
<div class="span9">Main</div>
<div class="span3">Pre</div>
</div>
or
<div class="row-fluid">
<div class="span12">Main</div>
</div>
I'm assuming you can translate that brief overview into PHP. And then you just need to put the PHP code to output the usual block and content stuff in the appropriate place. As a bonus you should get RTL for free with this kind of layout.
A next step that Bootstrap doesn't do by default (yet, I think they're possibly adding it in the next version) but can be done just with some CSS is to make the two block columns collapse into one column at narrow widths (e.g. iPad horizontal and netbooks) but before everything collapses to a single column at iPad vertical size.
I would have much preferred if BootstrapBase/Clean had used exactly this layout, so I'm glad to see someone experimenting with it. If I can help in any way let me know.