Right, each module (using SS modules) is a single RGB channel (3 pixelnet channels) ... you mix them to form the color you want ... and that module (all 3 5050 LEDs on the module) changes color.
Depending on the sequencing software you use, they may support RGB channel (groups of 3 channels mixed together) or be shown as 3 channels in a row (vixen, currently). Software like LOR S2/S3 or LSP support RGB channels, which just groups them into groups of 3 for you, making life a little easier and cleaner.
Note: The real power, IMHO, is in using grouping of RGB channels, and then running chases (or other effects) on them ... whether your using 'channel groups' in LOR S3 (not released yet) or using virtual controllers, layers or other grouping mechanisms in LSP ... LSP 2.0 is also soon to be released and supports pixelnet, whereas LOR S3 probably doesn't.