STM32F429 Discovery debug options
I have the same board and the top part actually contains the ST-LINK/V2 debugger/programmer. You can even use it to debug/program other boards by configuring the CN4 jumpers. There's more detail in section 6.3 of the User Manual here. It is extremely powerful and quite straight-forward to use in Atollic TrueSTUDIO or System Workbench.