Thank you. That's what I thought might be happening and it makes sense to me; any other way and the subplots will become too diluted. By keeping each one separate, each one truly becomes its own story. Then by being able to move the cards around the different acts, you could play with several different major plot lines without having to completely rewrite a particular scene. I like it.

Plus it becomes very easy to see if you've got too many beats from a single storyline [or for one character, if you're colour-coding by character] clustered together.

I use one color for the main character of each plot line, since i'm writing a script with 1 protagonist and 3 sub-plots each with their own protagonists that intersect with the main characters' storyline. My plots overlap so much I find it more helpful to use white index cards and simply color in little bits of them (or use different color markers) to correspond with the characters in the scene. Then I make sure all the colors are pretty even.
Adds a little bit of kindergarden-style fun to the not-so-fun (for me) task of plotting/outlining!

I just used index cards for the first time on a script! I used white for the plotline, and different colors for each of the characters/subplots. I guess I think of other important characters and their subplots as being the same thing - for this exercise.

This visual trick can also help for genre films. For an action movie, use one color for action sequences. Then a glance at your wall tells you the rhythm of your piece -- where you need to give the audience a breather, where you've gone too long without adrenaline.

@Gaffney: That's a great use, visualize the pacing of the story between action scenes and those more driven by interaction, revelation, dialogue.