We do the same thing with Zed Builds and Bugs Manager from Hericus Software.
We have to combine the .Net assemblies with C++ dll's and package the whole thing together into a Java installation (imagine that confusion :-) ). We also use FTP to upload some components of the build (not the whole thing) to other systems that need pieces of what the build produces.
After everything has all been rolled together, the nice thing about the Zed server is that it becomes our system where everyone knows where to get their artifacts from. It handles promotion from Dev to QA to Production, and tracks the builds through this lifecycle.