Endo-Steel doesn't really protect or cover anything. It's literally the structure of the 'Mech.
Ferro-Fibrous CAN be restricted to only covering certain parts through the Patchwork Armor rules, at which point the Crits that are used must go in that slot. However, in the majority of cases where all Armor is Ferro-Fibrous, they can go anywhere, as PLLP said. Not that it makes much of a difference except the amount of Armor one can install, as aside from 1 TacOps SRM Ammo type, F-F Armor is treated like Standard when hit.
Mostly it's there as a balance mechanic so some payment must be made in the set up for these lighter materials that doesn't go in to C-Bills. Having both makes it REALLY hard to fit 2 AC/20s in to a Spheroid 'Mech, for example.