I am at the stage on my 69 Dart of installing all of the body plugs. I bought one of the kits that has most, but not all of the body plugs so I am going to reuse some of the old plugs which is O.K. because many of them are actually in really good condition. However, I am having trouble figuring out where some of them go. When I disassembled the car, I took out many of the old ones and labeled them but some were left when the car went to the body shop where they were taken out and as a result, I'm not sure where they go. Many are the same size but some are rubber and some are plastic as well as some are the same diameter but are shaped differently (some are cupped while others are flat or solid). What I would like to know is, is there a reason why some of them are rubber and some plastic, and also, is there any sort of a diagram or schematic that shows which ones go where?

Can't answer you specifically to an A-body as neither of my current Dusters are stock/original, but judging by my last several B-bodies, the rubber plugs tend to be for the floors & firewall and plastic tends to be elsewhere.
There are exceptions: clutch-rod hole and quarter outer extensions (plastic). Flattish plugs were door vent-glass access. Trunklid underside plastic. On some models, trunk floor (over rear axle) plastic.
But you'd be best served by checking out an original Dart. Rick Ehrenberg @ Mopar Action & here may have a factory illustration.

Hopefully I will be at your stage of installing all the body plugs in my 69 Barracuda soon. I made a list of where all my body plugs came from - maybe they are close to the same as for your 69 Dart. My car was made at Hamtramck November 1968.

See the list in Excel here:

https://www.dropbox.com/s/8i8d14gqo0pwxjf/Layson%27s%20body%20plugs.xls?dl=0

Sorry, the spread sheets work for me, but I know it's difficult for others to decipher. Ignore the sheet named 'List with purchases' (lower left corner) unless you bought exactly the same replacement plugs that I did. The sheet named 'List without purchases' (lower left corner) will make more sense to you. PM me if any questions.

Here's a curious thing about body plugs. The floor pan for my car was stamped with holes for both bucket and bench seats. My guess is that all others were stamped that way too, but I have no information. In the case of my car that got bucket seats, the unneeded bench seat holes were plugged with four 5/8" plugs. When I tried to buy replacement plugs I was told there was no such thing. AFAIK nobody is selling any body plug kit with 5/8" plugs. There is no Mopar part number for 5/8" plugs, but there are part numbers for other sizes.

The top photo shows two 5/8" bench seat holes in the raised area. Two 5/8" bucket seat holes are just beyond at a lower elevation.

The lower photo shows a close up of one each bench and bucket seat holes with slight misalignment of the reinforcing bracket below and factory paint. So there definitely were factory 5/8" plugs, at least on my car.

Thanks for the help. I will use the info. in the spreadsheet as a reference for my car and see how it goes.

"is there a reason why some of them are rubber and some plastic"

When I was doing my car I was wondering about this as well. Couldn't see any consistent pattern for the use of each material.

Same thing on my 69 Cuda it has both sets of holes and mine were plugged as well.