OK.
First off, for most run of the mill units, you could just use the straight Battle Rating (BR) and be done with it.
Remember that EL already accounts for breath weapon and magical abilities and so forth; and definitely remember that for every ability you "extract" from the basic EL formula, the more impact that ability will have on the outcome, and the less "accurate" the system becomes as a predictor of "averages" or "multiple iterations."
In my experience, however, folks want to see a dragon roast an entire unit of footmen at once, so that's why these rules are there.
As you read through this example remember that what we are trying to emulate is the fact that a single creature with an area of effect weapon can apply its abilities against more than one opponent, instead of only being able to apply its abilities to a single foe at a time. Thus, it's as if there are more combatants in the unit than the unit size accounts for; and this is why the bonus for area of effect abilities is tied to table F-2.
Let's say we have a unit of 10 gorgons with a breath weapon that turns folks to stone. The range is 60 feet, the save is Fort DC19, the effect is, basically, save or die.
The gorgons have a unit size of 10, a unit size modifier of 6, and a Battle Rating (BR) of 20.
Now we look at table F-3 to determine the bonus they get for that breath weapon. Looking across the top to "Cone" and down the side to "60 feet" we see that the breath weapon could affect up to 63 Small- or Medium- sized targets.
(Just FYI, all table F-3 does, really, is calculate the area of an these various geometric shaped effects, and translate that area into a number of 5x5 target squares.)
The bonus you get to your attack roll is found by applying that result of Table F-3 to Table F-2; in this case, 63 targets translates to a bonus of up to +11.
Now let's look at two sample target units.
The first target unit is 100 men; each CR1, total BR14. Against this target the gorgon unit makes a Battle Check, 1d20 + 20 (BR) + 11 (area of effect), against a DC24 (10 + target unit BR14). If the check succeeds, the unit of men will lose 2 BR + 2 BR for every 4 points by which the Battle Check exceeds the DC. (It looks grim for the men.)
The unit of men makes a saving throw and, if successful, reduce the BR loss by 1/2.
Target unit #2 is a unit of 10 ogres. (CR3, BR14).
In this case, the breath weapon cone only affects, at most, (63 x 1/4) or 15 large creatures. (If you were to draw out the area of effect of this 60' cone, you have not quite enough room to put 16 Large creatures, each with a base of 10x10, into this area.) This information is found in note #3 at the bottom of table F-3.
Looking at Table F-2, the bonus for 15 creatures is +7.
But wait! There are only 10 ogres in this unit, so the bonus can be no higher than +6.
From here we continue as before-- the gorgon unit makes a Battle Check 1d20 + 20 (BR) + 6 (area of effect) vs. DC24 (10 + target unit BR); the ogres lose 2 BR + 2 BR for every 4 points by which the check exceeds the DC. (Still, pretty grim, but they also get a save.)
A couple of last minute notes.
1) Because a gorgon cannot breathe at will (they are capped to 5 times per day), they lose 1 BR after every breath attack they make. Remember that the BR represents more than just "hit points;" BR represents "resources" and the gorgon's breath weapon (and a wizard or cleric's spells per day) are expendable resources.
2) If either the men or the ogres were skirmishers, for example, they'd get a +2 bonus to their save against the effect. (Skirmishers put more distance between themselves within their unit formation, meaning it is harder to get them all under a single area of effect. Conversely, all of that extra space between allies means it is easier to flank skirmishers, so they are at a penalty in melee...
If you have follow up questions I will be happy to answer...
Wulf