Probably this is not the appropriate place to post this question, but I chose to do so, cause Ps users might
If you want a color to be more subtle, or put it another way, make it stand less among other element or/and colors
what you would to?
Increase opacity, reduce its saturation or something else?
This is an art/design question, not really a Photoshop question. "Subtle" is not one of the physical parameters of color. It is subjective and situational. Basically, any color is defined by 3 physical parameters: Hue, Value, and Saturation. Hue refers to its position on the color wheel. Value refers to its position on a black to white scale, or equivalent brightness. Saturation refers to purity/intensity vs a neutral gray of the same value, in other words, how much red is in this red? How "watered down" or "greyed out" is it? These 3 factors are theoretically capable of defining any color, but while absolutely necessary to know about, they will not help you to achieve subtlety. To approach "Subtle," we need to understand that what makes one color stand out or "pop" in relation to another is Contrast, and there are several forms of contrast: for example, warm/cool, light/dark, weak/intense are forms of contrast. To achieve subtlety, lessen contrast and use simple, pleasing color schemes. Good luck, and just know that the above items require years of study to understand, even by talented artists and designers.
In one paragraph you mentioned many important concepts.
I am just trying to achieve a good color balance in the web application I am designing.
Not easy at all. A bad color balance will convey the wrong message to the user-something very important.