In a fluorescence project, every channel is already an input. The User Manual lists the built-in images, the "Original" image in brightfield and the channel images in fluorescence, as what engines start from. To process three channels, you add the engine three times and choose a different channel for each.
The Image Data group of the Basic Operations Module handles 3-channel images. Extract channelLoading... takes one channel of a 3-channel image as a grayscale imageLoading..., chosen by Channel index (1, 2 or 3; default 1). Its variant Extract strongest channelLoading... picks the one channel with the highest average intensity: a whole channel, not a choice made pixel by pixel.
Going the other way, Set channels to RGBLoading... copies three grayscale images into the red, green and blue channels of one RGB image, and Swap channelsLoading... reorders the channels of a 3-channel image. None of these four changes the intensity values; they move channels around without touching the numbers inside them.
To build a new channel, Virtual ChannelLoading... combines selected grayscale images of the same type into one, for example a nuclear and a membrane marker. In brightfield, Color SeparationLoading... makes one channel per stain out of the RGB image.
For RGB color imagesLoading..., the three channels aren't independent. Together they encode color as a trichromatic representation, and converting to a different color spaceLoading... reshuffles them, sometimes nonlinearly. Fluorescence channels are closer to independent, since each ideally reports one fluorophore. BleedthroughLoading... between neighboring dyes breaks that ideal, and Spectral UnmixingLoading... exists to undo it.
Source: StrataQuest 8.1 Engines Reference, ch. 6.5 (pp. 166–179), ch. 42 (p. 544); User Manual §11.1 (p. 149), §9.1 (pp. 64–65); TissueFAXS 8.1 User Manual (p. 248).