Any singular scene plays out according to whether the scene's main girl is red or blue at the beginning and then your decisions within the scene itself. However, if a scene started "blue", you will not get the "red" content from it no matter your decisions within this scene.
There's different content in both parts however, so you'll always "miss out" on stuff, but also always will get stuff. There is no "right" or "wrong", no "good" or "bad" color. Just play as your heart desires. If you want to see all content, you'll need two runs, in that case the easiest way would be to go all blue in one and all red in the other, though in theory you can mix and match as you want. You can always mix and match different characters, so go red for Amana and blue for Amanda, or the other way round, or give them the same color.