Where is the regular wheel brake input on modern airliners?
The same way it is done in small airplanes and older airlines -- toe brakes.

The rudder pedals translate forward and back to actuate the rudder and they pivot around the lateral axis to actuate the brake system.  Each pedal independently controls only the brakes on its side of the airplane (e.g both pilots left toe brake actuates the brakes on the left main gear).  

Planes will often have an emergency or parking brake, which will be a lever somewhere that actuates the brake system.  This system, outside of emergencies is only used when the plane is not moving and you want it to remain that way.  

Larger airplanes with also sometimes have autobrakes which provide a triggered automatic application of a certain level of braking.  This kind of system is used both to provide automatic maximum braking for a rejected takeoff (RTO) and some lesser automatic braking upon landing rollout.  

To summarize, for taxi and ground movement the brake input is coming from the toe brakes.  When the aircraft is stopped, brake input will be transferred from the toe brakes to the parking brake.  When the plane lands, if it is so equipped and enabled, the autobrakes will begin brake application and the pilot will take over with the toe brakes and continue to use toe brakes for the taxi in.