When I painted my 66, I carefully masked off the upper surface leaving all the cowl vent slots open. Then, sprayed through the vent slots.  It worked great.

Then, when Mastercrap painted my car in 2010, they left all their sanding dust in there and did not bother to clean it out before they piled a ton of paint and clear coat on it to seal it as a trash pile for eternity.

In my opinion, flat black undercoat is the best thing to spray in there. It makes the area invisible to your eye. That way, a bright body color does not draw your eyes down into the cowl. Seems like the Eastwood spray can with a wand that reaches down inside is the best way to go

In my opinion, if you do not remove the top to gain full access to the hat area, anything you do is a waste of time because there will be a bunch of busted up seam sealer and existing rusty surfaces that won’t benefit from a blindfolded application of anything.

At minimum, remove the heater box and driver vent assembly and reach through the holes to do the best cleanup you can do. Make a bent paint brush so you can reach through the holes to brush (whatever you decide to use) on the perimeter of the hats.  I am a believer in using those plastic hat sections that you can RTV in place, just in case of any rust-through on the vertical sections. I have had them on my 66 for over 30 years now. Installed as a precaution.

BobE wrote:

I used Eastwood's rust proofing in the cowl area.  The fenders were removed at the time.  I used the wand (like 12-15" long) that Eastwood sold, and inserted in the holes at the ends of cowl.
My cowls were in good shape and were not replaced.
I'll note that I used that rust proofing pretty much everywhere (doors, rocker panels, frame rails, etc.) as the car was completely apart. 

Thanks Bob! What product did you use?

Toploader wrote:

Thanks MS. The cowl area was repaired 20 years ago and I did get paint all around that area. It's been garaged since then too. I don't think there would be too much trouble in there. I'm just being cautious more than anything...
With the plastic sections that you are referring to, are these it?

Yes, those are the ones.  Slathered with loads of high quality RTV