I have the navonics app on both my I phone and I pad. The location icon on the I phone seems to be pretty accurate, not so much with the I pad. At times I've noticed it's off by a lot, like 100-200 yards so I've always been leery of using it for way points.
The app works VERY well if you pair your iPad or iPhone with an external GPS device like the Garmin GLO. It uses GLONAS to update your position 10 times a second, is accurate to within a foot, and has no lag. It then connects to your iPad/iphone (or Android) using Bluetooth.
The Garmin GLO isn't waterproof, but can tollerate heat so I suction mount mine under the windshield where it has line of site for sky, no metal objects around to affect the compass, and is protected from rain. It's got a built in battery that lasts about 2 days on a charge (and has a USB port for charging, and it will operate while charging if you run a cable to it in the boat from a cigarette outlet, etc.)
The GLO is $100, but more than worth it because you can use it for more than your boat (works in a car or even an airplane too!).
It's especially perfect if:
1. You don't have a Fishfinder capable of using external Navionic's micro-SD cards
2. You do have a Fishfinder, but want something portable that you can use regardless of what boat or car you're in
3. You need a way to share your planned, present, or past location with friends/family (to show your spot, meet point, etc.) Using the App it's easy to set a point and take a screen shot, which a savvy user can then use to pinpoint your location on their mapping device. If the other person has the app too you can easily record, and share your location, your waypoints, your entire trip track including speed, direction, etc (like a DVR recording). It will send to the other user through their system online (requires internet or cellular to work obviously).
With the external GPS device paired (GLO) the iPhone app is perfectly accurate.
It should be stated too, that the Garmin GLO using Bluetooth can be paired to as many as 5 or 6 devices at the same time... meaning both iPhone and iPad can be connected, and anyone else in your boat that has GOOGLE MAPS (pre-downloaded... yes you can pre-download entire regions).
If you (or they) download the Google maps for your region ahead of time, then when you get mobile on the lake and lose service from cell, it has the data onboard the phone to map you. All it needs then is the GPS coordinates. The phone has a GPS anntenae built in, but as you saw yourself, they're often unreliable due to interference, etc.
Using the external GPS unit paired with bluetooth, plus Google Maps pre-downloaded (or Navionics & any number of mapping apps) provides a pretty damned accurate way of navigating and knowing exactly where you are with just a GPS signal (no phone service needed).
or are you setting the depth offset? 
hope that helps
