Short answer - it involves a lot of work.
Longer answer. You can't add individual tools, you add 'toolchains' - compiler, assembler, linker etc. This involves writing an Eclipse plugin and writing (a lot) of XML. When adding a toolchain, you can add you own tools to 'extend' the compilation tools.
More information can be found in the Managed Build System Extensibility docs:
CDT/Archive/designs/MBS - Eclipsepedia
What do your tools do - there may be a better (i.e. easier) way to do this.