Found more rust, what should I do?

Found more rust, what should I do?

This is what I have on the passenger side rear quarter:
000_0027.jpg

But now I found a small bubble under the paint on the driver's side, it is small, but I was able to poke the tip of a pen through it.

Should I replace the whole lower quarter, or should I just patch and weld it. I am worried about rust comong back. I was going to just cut a few squares out, then coating the inside of the well with rust converter, then sealing it with encapsulator, then paint. Will this work or should I chop out the whole bottom. There is no buildup of crud in the trunk wells, they are clean, so I am thinking that these started from external riock chips and spread.