questions on characteristics

I need some direction I have a product that has 5 different sizes small, med etc and then each size has a color however all sizes don't have the same color options but there are alot of color options.

I have the main product and then for characteristics I have

size drop down
color drop down

I want the user to display the size drop down and then the colors for that size to be shown in the color dropdown, no matter what I try I get out of stock message for the variant options that are not available. How do I make it so the second drop down of color will only show the available colors in that size

What is the best way to do this?

The simplest is to not use dropdowns but a 2 dimensional table display. You can change that with the option "Characteristics selection method" of the Display tab of the configuration.
That way, users will only be able to select existing variants.