For FAA logging purposes, the "sole manipulator of the flight controls" means the person who is controlling the attitude, speed and direction of the aircraft. This is the "Pilot Flying". And yes, it counts while the autopilot is engaged too. The other pilot operating secondary controls and appliances, radios etc is most often referred to as the "Pilot Monitoring" in most two-pilot operations these days. They are not the "sole manipulator" and may not log "PIC time" or "instrument time" while performing PM duties. Of course if they are the designated PIC, then they log ALL the time as PIC. If they are acting as the SIC, but they are also the PF, then under 61.51 they may log "sole manipulator" time as "PIC time" if they are rated in the aircraft. Any "instrument time" or "approach procedures" goes to the PF for logging purposes.
So now this should be just about as clear to everyone as Mississippi river mud!