No worries, PTv2 is not exactly user friendly. you are correct stop positions are optional, I tend to only use them at  start and end routes to give a nice place for the path to begin and end. with Merthyr bus stations the stop positions are already there so you might as well add this one. 

With the route master, i'm not sure if its required with only one variant, the wiki isn't clear. I've always just added it since its extremely simple to do compared to the route relation. 

feel free to have a look at the relations on the exit road of merthyr bus station. i've already mapped all but routes that start or terminate there. on side note this also shows one of my issues with PTv2 since that one road has 32 relations on it due to all the variants.