There is no reason why you can't do a great job with the stain provided in the kit. What I like to do, when using a water based stain, is raise the grain of the wood before staining, the whiskers will stand up, then sand everything smooth again, do your staining and lightly sand with some 320 grit sandpaper. I mean lightly so you do not affect your staining job. Then finish as usual.
Personally, I am not nutz about water based stains and finishes but you can still do a nice job with them.