I was playing in a 3-man group last night: Squire, Huntress, and Monk. We set up the same defenses on all 3 entrance points to the map. Squire walls with Huntress proximity/inferno traps in front, and whatever auras the Monk felt like using (not important to this example).

When the waves came, each of us defended one section. The Squire and Huntress spent most of their time repairing defenses (especially the Huntress's traps, which replenishes the quantity), and the Monk spent all his time fighting the enemies. The end result was that the Monk had the most kills, but let all his defenses die and leaked enemies through to the crystal.

The Huntress and Squire, by comparison, had no trouble holding off all the enemies, and the Squire even held off the Ogre. The Monk was not a team player, and leaked because he didn't repair the Huntress traps. The Squire kept the Huntress traps replenished and didn't even break a sweat.

tl;dr: The key to playing Huntress effectively is to have your teammates repair your traps. I'm pretty sure that's the crux of it.

I duo as a Squire with a Monk and we have run across this problem as well. After doing some testing, I definitely see the problem you are talking about. I hadn't run into it on live because my Monk friend found that pretty much the only way to solve this is to slightly skew the setup of the auras.

Overlapping Setup: Selling

Here you can see the problem you described. Everything is overlapping evenly, and the Snare field is inside the Lightning Field. Unfortunately, you are unable to upgrade or sell the Snare Field without doing so on the Lightning Field first. However, you mentioned your friend plays an Apprentice, and you are able to Sell whatever is inside these fields. Make sure you notice the icons next to your cursor, which will tell you which item you've selected. I highlighted those in the red box in the first 2 pictures.

Overlapping Setup: Repairing

When repairing with a perfectly overlapping set of fields, as far as I can tell through testing, the Repair icon will prioritize the field with the most damage. It's a bit hard to see, so I tried to zoom in the selected section, but the Snare Field has taken more damage than the Lightning Field, so even though the Lightning Field usually envelops the Snare Field, the Repair option prioritizes it.

And of course, if you hover directly over the Barricade itself within the two fields, it will be prioritized.

Skewed Setup

This is what we do. He sets them up slightly skewed. The distance between them is large enough that you should be able to relatively easily Repair, Sell, or Upgrade each individual field without sacrificing too much of the effectiveness you get by overlapping.

I've colored each field the appropriate color where they don't overlap, then showed an example of where you can hover in order to work with each item in the picture. I stood in one spot and moved my cursor to each separate area, then photoshopped them all into one so I didn't have to post multiple photos of just a moved cursor. With this setup, you should be able to more easily Repair/Upgrade/Sell on the fly without sacrificing effectiveness. It gets more complicated the more you have in the fields of course, but hopefully this helps! Unless they release a patch or something that allows you to select a field inside another one, this is what my friends and I do in order to make this more clear.