Modfactor MIDI control with Ground Control

I purchased the Modfactor because I was told that it would
solve my dilemma of having to drag a rack of effects with me at every gig.  What I want to do is have all of my guitar
effects/control in the pedalboard so that, like with the rack gear, I can use a
single program change to change amp channel, choose an effect and engage the
effect or, pick another program and have the effects bypassed.  I was told that the MF would do all of
this.  I also intend to pick up the
TimeFactor if this works out.  I have
however run into a few issues.

Granted, I?ve spent about 3 hours with the unit and the
manual, I have thus far not been able to control the unit the way it was
explained to me.  I hope someone can
help.

Example problem:

Program 01 on my Ground Control (GC) should be my amp clean
channel (Ch 1) and no effects (MF bypassed).  ). Ironically,
it does this out of the box. 
When I switch to program 2 on my GC, the MF engages program 2:1.  I don?t want that, I would like this to also
be bypassed.  I went into the MIDI
control and set the MF program for my GC program to ??? (i.e. nothing) and now it no longer switches the MF to program 2:1 (unless it was there
last) but it does enable the effect (what ever effect was cued up last).  So,
what it looks like is, I can assign an effect patch to a program change with my
GC but I cannot seem to control whether or not the effect is enabled or
not.  I found where I can set the Bypass
toggle in MIDI control but this doesn?t seem to correspond
to the specific program change from the GC.  It is kind of random. 

What I simply want to do is assign a MF program and set
whether or not the effect is engaged to a single program change from my
Ground Control.  (i.e. GC program 21 = MF program 3:1 and effect is engaged).  Can this be done or, is
what I?m experiencing how it really works (You can control the MF program but NOT the
program AND whether or not the program is on or off).

Can anyone give me some tips?