You can do it either way since the pipe is 4". If you use 4" pipe, the flange fits inside, so when you repour the concrete you broke up to move things you don't have to worry about making room for the flange to fit around the pipe as you would have if you used 3". Install the pipe long so you can cut it off once you get your finished floor on. Keep in mind that you may have to move the vent in order to make it work properly and meet code. The shower needs a 2" drain line. If you are thinking about tiling things, check out www.johnbridge.com you might also want to check out www.schluter.com and www.wedi.de about a couple of neat shower tiling systems.