Maybe do both: provide the ability to build basic pages etc, you probably already have a front controller mechanism, view templates etc so it’s within reach. Then make a plugin that allows integration and control from within wordpress. That way the wp upgrade issue (theoretically) only affects your plugin.
…but i don’t know anything about your software so I may be way off!
You need to fix your html – the header is not valid and there is an unclosed a tag – try the w3cv alidator at: http://validator.w3.org/ – it will tell you the exact lines that have problems.
You need to set the .narrowclumn and the first sidebar to float left. You shouldn’t need to float sidebar2 to the right. Don’t forget to take a look in ie5 because it is likely to mangle the layout!
Cheers
