As a general rule, the rocker panels, ie; the panels under the door sills, and the cowl will have drains holes. On some bodies the cowl/quarter panels will drain into the rockers.
I have made it a habit to flush out the doors, rockers, etc. with a water hose on a regular basis, especially on old cars as soon as I purchase them.
I have seen several bodies where-in the drain holes were plugged either from dirt/debris and/or body caulk that was applied when the body was built. An awl or phillips type screw driver are excellent tools to loosen the stuff that has plugged the drain holes....Bill

Thanks for the advice. Are you referring to the drains in the bottom of the door? Or in the door sill? I know about the drains in the door. Are there also drains in bottom of the door sill where the running board attaches?

Just remember- don't seal the water egress passage without sealing the intake.  IMHO .  Remember to clean out the drain holes and leave them as drain holes.

Thanks for the information. I will use the flexible chalking for the seams. I wonder about what to use in place of the putty that was shoved in behind the hinges and the insulation that was at the bottom of the door pillars?

In a general sense, you have to take into consideration the manufacturing process that was incorporated into the "Old Cars". The cars were built to last ten years at the outside, not the sixty plus years they have survived. Caulking and putty were used to seal out water and closeup unsightly gaps between poorly fitted panels.
A second factor that should be taken into consideration is, that in spite of what people think, not all workman follow instructions to the letter, especially if they are under time restraints. I have an unmolested '40 Buick sedan that has caulking/sealant on one side of the body.... none on the other side. I have a copy of a factory recall on the '40 Buicks to correct a water leakage problem in the rear seat area.... The correction was done on the left side but not the right side.

I would suggest that you go to a good automotive paint store and purchase body caulk. I have used a product made by 3M in the past that works very well. The automotive body caulk can be painted over, just like the original caulking....Bill

I am in the process of sealing all the joints and seams on my restoration. I have a question about the use of putty and chalking. When I took the car apart, I removed all of the chalking and other putty. There were big wads of putty that looked like black play dough in several locations. I am curious about the purpose of this putty and suggested replacement product.

First, there was a 2" to 3" wad of putty between each door hinge mounting bracket and the body skin that forms part of the front wheel well. Was this to provide additional stability for the hinge? I know it was putty because the impressions of fingers were obvious in the putty where it was pushed in.

Second, at the base of the door posts (both front and back of each door) where they join the door sill rail, there was insulation stuffed down in and chalking piled up on top of the insulation. I am guessing the insulation was to keep the chalking from running down to the bottom, but why was it even there?

Third, There was a piece of materials (like Styrofoam) about 3" long pushed into the door sill rail. Anyone know what this was for? Perhaps it absorbed sound that was transmitted through the door sill rail?

Fourth, there was another wad of putty shoved into the seam below the taillight where the body panel, floor pan and trunk lid lip corner all meet. It seemed this putty caused more rust than anything. Anyone know why it wasn't just sealed with chalking like the rest of the seams?

Thanks for any history or insight. This may be getting into the realm of the best opinion wins.

I am thinking of using rigid door post foam to fill the space at the bottom of the door pillars and behind the hinge mounting brackets. Does anyone have any thoughts on this? I don't think it would distort the body as the space is open on both the top and bottom to allow for expansion.