.htaccess rules and making wordpress play nice with code igniter

Hi Guys!
I'm hoping one of you with your giant brains can help me or give me some insight into this issue I'm having.

A client asked me to build a complete front end for him using wordpress - which I did and it runs beautifully - using some of the amazing plugins from here I might add

Unfortunately the 'backend' of his site was built by another company and they used code igniter to create it. I have no experience whatsoever using code ignitor other than knowing it is a cms.

So here's my issue - wordpress' mod_rewrite rules aren't playing nice with code igniter's since both of them use dynamic urls. I can get wordpress to ignore the physical directory in which the 'backend' is installed in but can't seem to get it to ignore the dynamic urls code ignitor is creating as well.

So I've put the following in my .htaccess and it works fine for the index file that code ignitor is using, (from /admin) but any of the paths that were created by code igniter (say /admin/advertisers) are still getting throttled by wordpress and throwing up a 404.

RewriteRule ^admin/.*$ - [PT]

I have searched and searched but I can't seem to find a solution - maybe I'm using the wrong keywords.

Also - quick side questions - is it possible to use the .htaccess to get wordpress to ignore subdomains altogether? Dynamic ones too?

This project is making me tear my hair out - what seemed very simple is turning into something way more complex.

Any help you guys could give me would be much appreciated - thanks in advance!