1. Physical aspects due to gender roles
We live in a world that is trying its level best to erase or ignore traditional gender roles. Mother Nature, however, established a number of differences. For example, as the "defender" or "the hunter," the male is generally larger, more muscular, has a thicker skull (all possible puns intended), and is more aggressive. Females are generally smaller, have mammary glands, and have wider hips for child bearing.
- Define the gender roles for your species and build some physical characteristics into the race. Terrestrial lizards are egg-laying species. If your species is, too, then the rectal tract in the female will accommodate this fact. If the females defend the nests, they may have stronger spring-muscles, sharper claws, or even a stronger jaw for combat. The males, perhaps still the traditional hunter, may have a leaner form for running and a neck gullet for storing transported food (not unlike a bird). The males may have a slimmer head and longer tail for running, the females a wider head and shorter, more muscular tail for defense.
2. Behavioral aspects
You haven't told us much about your race. For example, what are their mating rituals? What are their fears and delights? Humans, for example, have this quirky love for chocolate, greasy food, and The Beach Boys (well... my generation, at least).
- Both genders may preen for mating, but how do they do it? Your runners (the males) may want to show their legs while the breeders (the females) may want to show their affluence (I don't want to dwell on the sterotype, but think "good housekeeper." They'd wear costly clothing, seek quality weapons, etc., to show their status). Males may prefer a vegetarian diet while the females may prefer insects (higher protein).
I'm fond of a line from Warren Zevon's Werewolves of London, "I saw a werewolf drinking a Piña Colada at Trader Dick's, his hair was perfect."
I mentioned a bit about plumage in #2 (how they present themselves to others and why), but plumage also can be very physiological. Humans do their hair, wear rings, makeup, tatoo their bodies, and heaven only knows what else to both attract and express themselves. Again, generally speaking, men enjoy women with smooth skin and women enjoy men with rippling pectorals. Women with rippling pectorals and rough skin and men with smooth skin have for millennia been seen as "not part of the norm" and often shunned.1
Generally speaking, however, we're not like peacocks in that we don't have plumage that intrinsically changes by gender (i.e., there's not a hair color for women and another for men, like there are feathers for birds), but that doesn't mean you can't. As you said, you can use scale color (perhaps fancy for the gents, camouflage for the ladies and their nests). But you can also use scale size, dorsal spines (if your species has them), tail lengths (which I've already mentioned), length of snout/face, size of eyes... Heck, you can even do length or size of claws and digits.
Finally, a lot of analysis has been done on what defines "perfect human beauty." Face shape, eye size and placement, hair line, etc. You can do the same here. Perhaps the men appear (to their enemies) solid, serious, unfazed by their surroundings while the women appear wise, cunning, and perhaps even devious. Extremes in these attributes may be perceived by the species as "more attractive" (which would be an excellent addition to your storyline — attractive traits that make little to no sense to your readers because, well, except for politicians and lawyers, we're not
1 Yes, yes, yes... we live in a politically correct world where some will be upset that old stereotypes like this are brought up. Except that any anthropologist worth their salt will tell you that these things are real and require a sophisticated level of reasoning to socially overcome. Please keep that in mind before winding up for a scathing comment that doesn't actually have much to do with the OP's question.