This might be a total noob question but I wanted to ask what are the best practices in creating builds for
Googleplay and Appstore? Should I be creating different project files targeted towards the diffferent platform or should I just create one project file and switch it as I build it?
That is one of the major benefits of using Unity. You can have one project, and target both Android and iOS. So create one project, and switch as you build it. You need a Mac of course to build for iPhone.