first thing you have to do is make a new tempate file, then copy
includes/templates/template_default/common/tpl_main_page.php
to
includes/templates/your_temp/common/tpl_main_page.php
then open that bit of code up to see how Zen aranges information and the 3 box layout.
then also copy the header and footer files and look how they work.
then you will see where zen places information.
then you will need to build a 4 cell table(or CSS), as follows:
<!--body table -->
<table class="yourtableclass">
<TR><TD colspan="2" name="header">
Header code
</TD>
</TR>
<TR><TD name="leftnav">
Left bar content
</TD>
<TD name="body">
Body code
</TD>
</TR>
<TR><TD name="footer" colspan="2">
footer contet
</TD></TR></table>
obviously enter the php from tpl_main_page to the spots you want it and change widths and lengths.
tpl_default_left holds the information for the left bars(the layout and whatnot)
change those files as you like and you will start to see how easy it really is to change everything.