I have found that it works best if you cut your freezer paper off the roll in the same size as a sheet of paper. Then iron it to your ironing board on a LOW setting (I use 4 out of 7), this will flatten the paper for you while still maintaining it's stickiness because it was a low setting. Then feed it through your printer just like a piece of paper. It should be fed through so the papery side (not the shiny side) gets printed on. It should not matter what type of ink it is since you are printing on the papery side, it prints just like it does on regular paper.
You can also buy pre-cut freezer paper sheets which are already flattened and feed through easier. I personally don't use them and have never had a problem, but it is an option. Those sheets can be found in a quilting store or joanns or something.
Good luck!
Rachel