How to program Xbee OEM series 2 Modules

We are doing a wireless sensor network project using Xbee modules as our University Final year project. We have bought some Xbee Series 2 modules and Two XBIB-U-DEV (and XBIB-R-DEV) development kits ( USB and RS 232)
The was a small software came with them in a CD. Its called as X-CTU. It only has a range test. We couldn’t programm motes as we wish through that development kit.Is there any IDE to do that? Any software?
We are confused how to do that.Please be kind enough to help us!!!