Hey DrathVader. I'm doing the same as you. I do the design in Flash Professional CS6 and after that I export to C2. The same as you, my characters become crop. Then, with Flash, I choose to export as PNG sequence. With C2, I go "edit animations" and "import frames". After all this, I crop all the images and this is nice because reduce the size and mantain the origin point. This works for me, even if it's a longer procedure.
I explain to you all this because I want to ask you something. I hope you know the answer.
Do you know if with the way I do it I use more memory than with your way? I mean, when you import a sprite strip, finally you get the same amount of images in the editor than if you export every image. I'm a little bit confuse with this, because I read in some tutorials that's better to import sprite strips than single images.
Otherwise, I will take a look to your link.