It can be done both ways, some people do needle turn applique with the freezer paper on the right side of the fabric, me... Iv'e never been able to master that technique :lol: so I use the frezzer paper on the reverse side of the fabric as you described.
The main thing to remember with doing that with a pattern that has been designed to be used the other way is that you will have to make a mirror image of all your pieces that are not symmetrical. Easiest way is to turn pattern over, trace the lines of the pattern pieces on the back so you can see them easier, then trace onto the non shiny side of the freezer paper. I hope that long winded description makes sense :D But I bet someone else on here has a betta way of doing that :wink: