Hey,
1. Yes, you can just export from construct2 and override the project files. I never close the project for that and it works fine.
2. In that case "Same" means your apk has to have the same ID (com.yourdomain.yourgamename) and needs to be signed with the correct certificate. There is also the version number. If you have exported with cocoonjs bevore they had set it up every time you compiled your game. In Intel XDK you can set that number by yourself. If you are not sure you can just type in there "100" and then every update plus one. It doesn't have to be in order but always be higher than the apk deployed before.
3. I don't really get what you mean by that. Just use ID (com.yourdomain.yourgamename) for all your games. It doesn't matter what platform (android, ios, tizen, windows phone,...) This should be always correct then.