It is good practice to run separate updates for the internal/external controllers, as they "can" have differences in firmware. The payload for both updates in THIS version are the same ... one update may update both, but I suspect it will only update the device it was intended for.
My Dell PowerEdge R710 has both the PERC 6/i and PERC 6/E installed. Both with active RAID arrays. I'm doing a system update (BIOS, iDRAC, Lifecycle, OpenManage, and PERC firmware). I notice that I've downloaded two firmware DUP files for the PERC 6/i and 6/E and they appear to be identical in every way except name. Do I run both? 
PERC 6/E and PERC 6/i Firmware Download - Is this actually the same file?