I hope I understand what you need.
In your skin file, the state upAndSelected is what you need to specify the color when the togglebutton is selected. You can copy the generated skin code from Flex to modify it or check the code below. Add it below the </s:Rect>
tag under <!--
layer 2: fill @private-->`
<s:Rect id="fill2" left="1" right="1" top="1" bottom="1" radiusX="2">
<s:fill>
<s:LinearGradient rotation="90">
<s:GradientEntry color="0xFFFFFF"
color.upAndSelected="#333333" // you can modify color here
alpha="0.85"
/>
<s:GradientEntry color="0xD8D8D8"
color.upAndSelected="red" // you can modify color here
alpha.downAndSelected="1" />
</s:LinearGradient>
</s:fill>
</s:Rect>
Paste the code above under
<!-- layer 2: fill -->
<!--- @private -->
<s:Rect id="fill" left="1" right="1" top="1" bottom="1" radiusX="2">
<s:fill>
<s:LinearGradient rotation="90">
<s:GradientEntry color="0xFFFFFF"
color.selectedUpStates="0xBBBDBD"
color.overStates="0xBBBDBD"
color.downStates="0xAAAAAA"
alpha="0.85"
alpha.overAndSelected="1" />
<s:GradientEntry color="0xD8D8D8"
color.selectedUpStates="0x9FA0A1"
color.over="0x9FA0A1"
color.overAndSelected="0x8E8F90"
color.downStates="0x929496"
alpha="0.85"
alpha.overAndSelected="1" />
</s:LinearGradient>
</s:fill>
</s:Rect>
Hope it helps.