For starters you can’t assign an audio plugin to a MIDI track. Get that out of your head. It’s total nonsense. MIDI triggers sounds/controls somewhere else. That’s all. No sound. Just triggers and stuff like SYSEX data. Repeat … no audio.
So, the next thing we need to figure out is if you are using instrument tracks or are you using the a VSTi loaded in the VSTi Rack (F11). Your capabilities for assigning FX to the output of various VSTi will be determined by which of these two methods you are talking about. Instrument tracks are totally restrictive, they simplify the process of creating tracks that control VSTi, at the cost of both people actually understanding what is happening and restriction of some features.
Finally, I am going to assume what you really mean is that you are using an instrument track and a VSTi like Kontakt that lets you load more than one sound, but you can’t figure out how to have a single MIDI track trigger different instruments loaded in Kontakt and/or you can’t figure out how to send the mutliple instruments to multiple audio outputs, so that you can put the effect on just a single patch.
MIDI … you can set the MIDI channel for each note individually in pretty much every MIDI editor. You can even have 2 C3s one on top of the other, with one going to MIDI channel 1 and one going to MIDI channel 2, both going to a single VSTi.
Audio. When you hit F11 and load a VSTi, there is a clickable little box next to the name of the VSTi, just to the right of the ‘e’. Clicking this will provide you a drop down that allows you to enable extra outputs if the VSTi supports them. Then it is a matter of setting up the routing inside the VSTi so that the individual sounds go to the outputs you enabled. THEN you can put your effect on a single output of the multi-VSTi that is controlled from a single MIDI track.