It sounds like you are an experienced DM, who has been successful so far without using the EL/CR rules.
That being the case, I don’t think they’ll help you.
Monsters’ CRs are often terribly inaccurate. Monster Manual II is particularly egregious, such as the CR 9 Adamantine Horror that has at-will Disjunction. Dragons are under-CRed almost by tradition. Numerous monsters are actually pushovers for their CR, particularly monsters whose CR depends primarily on their relative lack of vulnerability.
Perhaps the best example is the Allip Allip (a 4 HD, CR 3 Undead) and the TarrasqueTarrasque (a 48 HD, CR 20 Magical Beast). The Allip is incorporeal, and the Tarrasque therefore cannot touch it. Meanwhile, the Allip deals Wisdom drain, which is one of the few things the Tarrasque is not immune to. A fight between an Allip and the Tarrasque ends with the Tarrasque unconscious, every time. (or the Tarrasque running away from the scary ghost, but the description of the Tarrasque suggests that it’s literally incapable of considering retreat; being an Int-3-incarnation-of-rage-and-destruction will do that)
The Allip is under-CRed; few 3rd-level parties have a good way to deal with incorporeal enemies, and Wisdom drain is phenomenally dangerous. The Tarrasque, though, is over-CRed – while it’s very difficult to hurt, it does have vulnerabilities, and for 20th-level characters, protecting oneself from the Int 3, grounded, and corporeal Tarrasque is not a great challenge.
Actually, since a low-level Cleric can rebuke Allips, and a low-level party can pool their funds for a Candle of Invocation, for a smart/optimized party, the Tarrasque could literally be closer to CR 3 than Allips are...
And then there is the fact that party power varies immensely. A 20th-level Wizard can stop time (time stop), has the most powerful creatures of the multiverse at his beck and call (gate), and can literally create his very own demiplane (genesis). A 20th-level Monk... can use feather fall at-will, but only if he’s next to a wall. These are not particularly close.
So CR rules aren’t very useful. Monsters have wildly differing power levels, even at the same CR. And parties have wildly different power levels, even at the same EL. Unfortunately, the best a DM can do is simply know his party and know his monsters, and try to find a certain level of compatibility.