Make sure you select Plug for Number 1 Trigger along with the settings for the

ignition type, Number of cylinders, and firing order.

The Gray RPM/Cyl1 lead is used to sync the Ignition Scope to Cylinder #1. It connects
to the 9 pin connector on the unit and to the #1 plug wire on the vehicle
This allows the Ignition Scope to display the cylinders in the correct position on the
screen.
There arent any other settings to adjust when using with this lead.
The signal from it is not displayed on a channel.
It is basically an external trigger for the scope and is also used for RPM calculations.
To determine if the signal from the RPM lead is ok, disconnect your secondary lead
from channel1 and only connect the RPM lead.
If RPM is displayed consistently and matches the engine RPM, you have a good
usable signal coming in from the RPM lead.
If it is not, try moving it to a different position on the plug wire.
The reason you have to remove the secondary lead for this check is the signal from it is
also used to calculate RPM.
The only other setting specific to Ignition Scope that may need to be adjusted is the
secondary detection threshold.
It works the same as on the Vantage Pro or Modis.
It sets the sensitivity of the ignition scope to detect ignition firings input to the scope on
Ch1 (Ch1 and 2 for Waste spark ignition) from the ignition lead.
It does notwork like the signal level based trigger in lab scope where the exact level
that will trigger the scope is set.
It takes into account other characteristics of the secondary waveform than just the
level.
The setting is displayed along the left side of the grid as a right facing triangle. It can be
moved up and down as needed. You can drag it or move it using the control on the
Trigger Setup window. Higher = less sensitive, lower = more sensitive. My rule of
thumb is to set itat the average spark voltage to start (Typically 1-1.5kV).
If it is set too low, the scope may detect events on the waveform that are not firings
such as coil current limiting in the dwell section, the start of dwell, or oscillations.
If it is set too high, it will miss cylinders.
There are some examples in one of the appendix sections at the end of the Modis
manual found here:
http://www1.snapon.com/diagnostics/us/UserManuals

The best thing to do once you get a vehicle connected and working correctly is to move
the threshold down until the pattern starts to break up and observe what happens.
Move it up until it stabilizes, then continue moving it up until cylinders drop out and
observe what happens. Once you observe this, you will have a much better idea how it
works and needs to be set.

You can typically find a setting that works ok at all engine speeds. In some cases you
may have to decrease it a bit when running at speeds above idle.