The HT section (transport/volume/channel/menu/pip) defines which devices you use when the remote is in "My System" mode. Common settings are to set transport to VCR, volume to receiver/amp/tv, channel to tv/sat/cable, menu to tv/sat/cable, and pip to tv. choose the appropriate setting that works for you.

The VPT section sets Volume Punch Through for a common device. Common settings are status to "on" and device to receiver/amp/tv. The other settings let you remove punch through for individual devices. For instance, you want to have your receiver control all the volume functions for your home theater except when you watch tv. You would set devices to amp (or rcvr) and set TV VPT to "off". Your remote will control the amps volume in every mode except tv where the tv will control its own volume. Note, mute is included in the
VPT mappings.

The extra "virtual" device keys (db-08 to db-14) are useful for adding codes to devices that you don't use often and don't want to waste a whole "real" device key. I only know how to access them through macros though, maybe somebody else can answer if there is another way to access them directly.