ATP CFII MEI

With flaps full and gear down, the autothottle (AT) flies 140KIAS and it will hold this speed until 50ft AGL, whereupon it retards the throttles for landing. But, there are Vref and Vapp between 140KIAS and 50ft AGL, and 140KIAS is usually way too fast over the threshold. How to tell the AT to forget about 140KIAS and instead fly Vref and Vapp? All I've heard anyone say is "select Vref" or "select Vapp". HOW??? What exactly is the procedure to "select" these speeds (I know how to generate them and select them in the FMS, thus sending them to the PFD) and -- most importantly -- have the AT fly them on approach?