I know of a number of different entrances to the Track 5-6 platform from various parts of Penn Station. This site contains a set of nice maps detailing the station layout, indicating the entrances to each platform from the concourses.
An Amtrak train's track assignment looks like this:
I haven't been able to find any reference for what the Gate assignment refers to. I presume that it means only one of the entrances to the track 5-6 platform are open, but I haven't been able to figure out which "Gate" is "W". (Presumably "West", but relative to what, given that there are at least three entrance locations to this platform on the Amtrak side of the station?)