I am not sure what you are trying to do. You could be trying to change the entire video to black and white except for two objects where one is red and the other is blue. It that is what you are trying to do it will probably involve some roto and a duplicate of your footage.
You could be trying to change the video so that the lighter tones become red and the darker become blue. Please explain precisely what effect you are trying to achieve and post an example. Even an example using one color would help.
Sorry, I will give you a example -
Its back and only the rose is red, this is what I want to do, but instead of using only the red, I would like to highlight a couple of things in blue in my own video.
So, if you take the above video, at the time 2.27 to 2.30, where you see the rose red, how would you get the leaves which are below the rose blue?
I already know how to do the black and red effect.
Im using after effects CS5
The Rain and Roses clip is using one color, and I take it you can do that effect in AE. What you need to do is to now duplicate your layer and change the leave color effect to blue and pick another subject. Now you will have to either create a procedural matte or roto by hand the blue subject letting the red subject show through. It's a matter of layering and masking.
You can even achive what you want in PrPro by keying out respective colours. See e.g. this Ann Bens's tutorial:
The procedural matte I was referring to includes keying. If you post a still frame of your original video with a description of the action, we can give you an idea of the easiest procedure in AE. Just as in the Premiere Pro tutorial, a minimum of two copies of your footage are required. The best technique depends entirely on your shot.