My girlfriend's iPhone is a bit off on the GPS part too.. not sure what's with that. I have the 3GS, maybe it makes a difference? But it never had an issue of pinpointing me in the exact spot I was in.
One really cool feature of navionics is that you can take a picture and it'll tag it in the app. So you can go back over where you were, or just keep a log of what an entrance to a harbour looks like etc and be able to look back on it later or another time you go there.