How to stop wheel well rust
 

On the outside of the wheel wells, on the flat spot I'm noticing a few very small paint bubbles, about the size of a pencil lead. Whats the best way to stop this before it starts rusting?
I bed-lined my rockers, could I do the same there? Or since it rusts from the inside out, will be just rust be hide the bed liner?

If it's that same as my truck, it's rusting from the inside out. If your already seeing it come through the paint, there is not much you can do other than replace the panels. I tried to grind out the "small" rust spots on my wheel wells and the deeper I went the worse it got. A complete bed replacement would be my next step...

clean and grind out rust and fill holes with wirefeed welder and sheet metal,if you have the resources.

Putting bedliner in there is not a good idea. You will trap moisture and salt against the metal.

When you're all done with any bodywork (if any), drown the wheelwell (inside) yearly in ATF. Remove the foam that Ford carefully installed in the seam, too. You may also use gear oil, thinned slightly with kerosene. Thinning the oil allows it to creep into the seam. This is a messy, but worth the effort.

Where is the foam you speak of? Whats the best way to get to it?
I'll check it out later tonight, the passenger side there isn't even any bubbles, its only on the drivers side. I think I counted 3-4 bubbles the size of a pencil lead. I ran my finger against one, and the paint bubble popped like a zit and water came out.

I would spray some used oil in there. This is what I do to my wheel wells and only time will tell if it works or not.

if you don't mind changing the look a little, I just cleaned all the corrosion off of the wells, painted it with some industrial grade anti - rust paint inside and out, then put fender flares on. It's a good way to prevent it from getting worse and covering up the already damaged paint

They do sell paint-able metal patches that can be welded in by a auto body shop
Most common to happen in the bed sides than the front fenders