Can't say for sure on the iPad,, but on my Android phone, there is a Remote Icon in the upper right corner.
Hit that and you should get an option to pic which STB you want to control.
Will probably have to use the regular remote to accept connection the first time.
Note: You can only do this while at home while you are connected to the same network as your STBs.
Just used the remote on the FiOS Mobile app to control my TV.
I'm running FiOS Mobile Version 3.5
Ipad 2 with iOS 8.1.3
If you have above 2 installed suggest you turn off the iPad completely and then turn it back on.
That worked for me.
Please post your results.