The ERJ Flight Guidance Controls are in the same place as the Boeings are, just the indications of what you have selected are on the Primary Flight Displays (PFDs), ie. the six pack of instruments. Selectable items like altitude, VS, speed, and heading are all indicated in blue on the PFD.
So, in a Boeing, when you set an altitude, it is shown on the FGC panel. In the ERJ, you set the altitude in the same spot as the Boeing, but the selected altitude is displayed over the altitude tape.
Ergonomically, I can't say either is better. The ERJ has its advantages, as does the Boeing. Honestly, combining both would be best, but would take up a lot of panel space. The ERJ has a very "clean" cockpit compared to many.