[Roadsters] Inner fender rust repair and proofing

[Tim]

I am about half way through the process of rust proofing and rust damage repair of the inner fender wells. During this process I have noticed that where the A-pillars are welded to the rocker panels, I see little gaps on the corners. While rinsing off the Marine Clean and metal etching acid with soapy water, etc, I ended up getting water inside the A-pillar. I can make sure the inner areas are dry.

One question is this: Should I close off those little holes (and any other similar spots) with the POR15 or a seam sealer? Or would it be better to leave them open so any water that gets in can then drain back out? I am leaning toward sealing any thing that looks like it should be.

Also, there are two hollow areas on the inner fender, below the cowl drains and in front of the A-pillars. One is horizontal; the other is at about a 45 degree angle. Both of htese have what appear to be built in drain spots and the angled area has two holes drilled in addition to the drain. 

What is drained out of these two areas? Is it incidental water that gets in through the unsealed seams? Can I go ahead and completely seal these hollow areas?

Thanks.
Tim