I have a 98 Mazda 626 GF and I'd like to test the ignition coils with a multimeter to see if any of them are starting to fail. The car has ECU controlled timing / ignition and there are two coils, each one servicing two cylinders I assume.
To be honest you won't get far with a DVOM. While vini_i's answer is correct you can't do this while the car is running.
You should be looking into buying a digital storage oscilloscope if you want to test primary and secondary ignition.
The uScope is a good beginners scope:
Along with a low amp probe for testing the primary ignition coil:
And a secondary ignition probe:
You would have to set the scope to the scale of the probe most low amp probes are something like 1mV/A or 10mV/A. And clamp around the power wire to the coil.
An example of a known good primary coil on a 05 VW Touareg:
And an example of a known good secondary reading off a 05 Ford Taurus:
And here's a good article on ignition diagnostics.
There are three tests that can be preformed using a multi meter.
A DIS type coil that services two cylinders works like a transformer. The primary windings are controller by the ECU. The secondary windings are the output to the two cylinders. The primary and secondary windings should never touch.
Using the ohm function check the primary and secondary sides for opens or very high resistance. It is generally a good idea to compare multiple coils that are on the vehicle. If one of the windings is open the coil is most likely completely dead.
The thirds test requires having a multi meter that supports conductance. Many high end Fluke multi meters support this function. Conductance is the reciprocal of resistance. When using the ohms function and the leads aren't touching the meter reads OL. When using conductance the meter will read OL when the leads touch.
To test the insulation between the primary and secondary windings set the meter to conductance. Touch one lead to the primary and one lead to the secondary. The meter should not read OL. If it does then there is a path between the primary and secondary, kind of like touching the leads together. If the meter shows numbers that jump around then the coil is fine.
If you are looking for misfires then you best shot would be is to hook up a scanner tool, start the car and go through the statistics in the scanner which shows you about the misfires and a lot more data, buy a good scanner which costs about $80 but don't go with a cheap $20 one.
The misfires should be less than or equal to 5 in every 1000 if not then you might have to change the coil pack or fuel injector in the particular cylinder. most of the times the spark plug or the coil pack would be bad and these are not expensive when compared to a fuel injector.