Petrockblog added it into his own fork of emulationstation so it is built into the default emulation station controller configuration which renders the inputstation script redundant. A full binary install should incorporate it. Make backups before just in case.
As far as I understand it (I could be wrong) it will be built in to the default controller configuration option in emulationstation- the functionality will basically be the same as the current input configuration you see when you first boot into emulationstation but there will just be more button options, you could try building from source or you could make do with retroarch joyconfig until there is an official release (which they may be waiting for to add it in its entirety.) As it stands its really no different than using retroarch joyconfig- it just enables one to configure controls in one step instead of 2 or 3. Eventually it will incorporate more non-retroarch emulator specific controls.
As far as a graphical interface involving specific controllers- I think in the future it would be cool to incorporate interactive controller diagrams similar the ones on the wiki but it might be a while before that can be done.