The IDE itself would exist outside of Scratchbox, because SB is really just a system for cross-compiling and testing, not for actual coding. A lot of IDE's, like Eclipse or ESBox, have support for compiling things in the Scratchbox environment, but they themselves exist outside of SB itself.

To actually get it to work, I presume you have to get some sort of plugin to tell whatever IDE you're using to use Scratchbox instead of the toolchain that is natively resident on your system. But, I don't use anything like Eclipse, ESBox, or QtCreator, so I wouldn't know exactly how to set those up.