Let's look at a sample monster and a specific template. So to illustrate I'm going to add a half-dragon template (CR +2) to a crocodile. This monster has worked well for me in the past.
Black Crocogon CR 4 (XP 1,200)
N Large dragon
Init +1; Senses darkvision 60 ft., low-light vision; Perception +8
AC 18, touch 10, flat-footed 17 (+1 Dex, +8 natural, –1 size)
hp 31 (3d8+18)
Fort +9, Ref +4, Will +2
Immune sleep, paralysis, acid
Speed 20 ft., fly 40 ft. (average), swim 30 ft.; sprint
Melee bite +9 (1d8+8 plus grab), 2 claws +9 (1d6+8) and tail slap +4 (1d12+4)
Space 10 ft.; Reach 5 ft.
Special Attacks breath weapon (3d6 acid, DC 17, 1/day), death roll (1d8+12 plus trip)
Str 27, Dex 12, Con 23, Int 3, Wis 12, Cha 4
Base Atk +2; CMB +7 (+11 grapple); CMD 18 (22 vs. trip)
SQ hold breath
Environment warm rivers and marshes
Organization solitary, pair, or colony (3–12)
Death Roll (Ex) When grappling a foe of its size or smaller, a crocodile can perform a death roll upon making a successful grapple check. As it clings to its foe, it tucks in its legs and rolls rapidly, twisting and wrenching its victim. The crocodile inflicts its bite damage and knocks the creature prone. If successful, the crocodile maintains its grapple.
Hold Breath (Ex) A crocodile can hold its breath for a number of rounds equal to 4 times its Constitution score before it risks drowning.
Sprint (Ex) Once per minute a crocodile may sprint, increasing its land speed to 40 feet for 1 round.
According to the rules, the Black Crocogon should be CR 4 which according to the monster statistics table he should have:
A slightly lower AC, more hit points, about the same attack, his average damage (bite, claw, claw, slap is 41 [double average] suggested for high attacks, his breath weapon is lower than normal; the base crocodile was almost twice its suggested value as well.), The Primary ability DC is high, and the Good Save is high.
Overall, the Black Crocogon deals damage as a CR 5, but survives hits like a CR 3. So overall, I think he's an okay version though I would like him to be more even.
At my table, I would probably drop his strength a bit to moderate the damage somewhat but add a couple of hit dice to boost hit points and breath weapon.
If I wanted to toughen him to a full CR 5. I would at least 2 HD to him and add a +1d4 acid to his bite and death roll from acid oozing teeth.