You can flash directly from IAR using their Segger J-Link interface. If you install the SDK making sure to select "Custom installation location", you should find an example IAR project in C:\Nordic Semiconductor\nRF51 SDK_v5.1.0.36092\nrf51822\Board\nrf6310\s110\ble_app_hrs\iar, that you can use as reference for how to set up this.
Perhaps I misunderstood you. If you want to sue nrfjprog to program a softdevice, this is completely independent of the IDE you use. nrfjprog should work the same, no matter if Keil or IAR is used. However, for downloading an application while developing in an IDE, I'd recommend you to not use nrfjprog, neither from IAR nor from Keil, as using the built-in J-Link support gives a nicer user experience.
