WordPress Output to Different Window

I am trying to embed WordPress into a Joomla system and I am just about there except both my WordPress columns are in HTML IFRAMEs.

Is there a way to redirect all WordPress output to a different HTML window. Sort of like a STDIO redirect.
Is all WordPress piped through the same function???
This is where I am so far.

http://www.acuitynv.com/joomla/index.php?option=com_wrapper&Itemid=26

TIA.