The secondary throttle plates cause a proportion (a large proportion at low throttle settings, and progressively less at high throttle settings) of the air/fuel mixture to be diverted along the length of the secondary intake manifold and back, to preheat the mixture in an attempt to reduce emissions. Full details are contained in Section Q of your Service Manual.
Removing them improves the responsiveness of the engine, and many of us have done so. How you do this depends on how much effort you want to put into it. Just disconnecting the secondary throttle shaft and jamming it into the wide open position provides much of the benefit for little effort. There are two threads in the archives that describe how to do this. Peter Crespin’s original dates back a few years, and a recent one describes a different method for cases where Peter’s method did not work for some reason. Search the archives for “Strangleberg” and you’ll probably find both. Here they are: