What differences in performance can I expect to see between these two GPS pucks?  I have an 1197 with a 16 channel, looking to go to a 50 channel.

The 50 channel will give better accuracy and lock on the satellites quicker on start-up.

Compare your unit GPS Diagnostic view with this one using the 50 channel.

so more satellites means more angles for position fixes.

16 vs. 50

Does this translate into better waypoint location? I haven't really had a chance to use it yet, because I just bought it.

Is the accuracy an issue with the 16 channel? It's not gonna be 20 feet off is it? or are we talking about the difference between 6 feet and 3 feet?

Accuracy is relative. In the diatance around the globe, a mile is pretty close. Saving a waypoint and returning to that waypoint exactly is dependent on the amount of error you have when saving it and the amout of error you have when trying to return to it. The larger the EPE you have, the farther off you can be.

The example I posted shows 2' EPE so that can be up to a 4' error when returning to the saved waypoint with the same 2' EPE.

I did this in my garage, with the 24' EPE, that could result in a 48' error when trying to return to a waypoint using the same EPE.

am I reading that right? It says 24' epe = 48 INCH error? I'm assuming you meant 48 FEET right?

That's a lot of error.  You'd be WAY off trying to find a laydown in deep water.

Yes, its 48' , I'll correct it. Thanks

You have the equipment to negate that error using Side Imaging. You can be 600' off and find it since you can cover 300'+ on each side of the boat when scanning.