It is a bit confusing at first, but once you understand some basics, I think you can see how it works. An "Interval Scaling Calculator" is provided in the Scaling Wizard inside CTRIO Workbench to check your settings.
First, I would advise that after selecting Edge Timer that you configure it for "Free Run". In this mode you do not have to reset the Edge Timer to get the next value, it automatically resets. Next, select "Interval" as the Scaling type. Since you want an accurate representation of slow RPMs I would recommend using Integer x100 (2 implied decimal places). This will give you hundredths of RPM accuracy in your reading if you need it.
Next, if you have an encoder that only gives you 4 ppr (pulses per revolution) and you are measuring RPM, this is not much resolution to work with. But taking that as the given; then consider RPM simply means "revolutions per minute". Thus running a 1 RPM with your encoder:
1 RPM = 4 pulses in 1 minute
Thus if you selected "minutes" as the Unit Time Base, then the Counts/unit would need to be 4 because at 1 RPM you will get 4 counts / minute.
We can check this using the Interval Scaling Calculator provided in the Scaling Wizard. Notice you can only enter pulse times in µs (microseconds). So, again, running at 1 RPM, I am getting 4 pulses per minute or:
60 seconds / 4 pulses = 1 pulse per 15 seconds
and...
15 seconds = 15,000,000 µs
Thus, if you enter 15000000 into the Pulse Time of the calculator you will see that you get 1 RPM. Of course, if you picked the Integer x100 (2 implied decimal places) as I recommended, the calculator will show 100 RPM which really means 1.00 RPM.
Does this help?