That's nice that the Canon software lets you take DNG images, interesting.
But to your question, no. DNG images cannot be changed or altered. Only the interpretation of the images can be affected by such applications as Adobe Camera Raw or Lightroom. To combine them would be to change them.
To do what you want is possible if you save them out as TIF or PSD images but then you lose the ability that DNG provides.
So yes, your 2nd solution is the way you want to go.
To save them, if you use TIF or PSD you will get the best image. If you save as JPG, you will then get JPG degredation and you do not want that.
As an aside, Once you make your composit image, any subsequent enhancments should be done with layers. Do not make changes on the original image and save that. Here's why: Let's say you want to get rid of the fire hydrant on your front lawn. So you take your rubber stamp, fix it, save it, and your done. It looks "OK." But later you learn about "Content Aware Fill" and want to see if that will give you a better result. Well, it's too late, you can't test this on that fire hydrant because you saved over that part of the image, you're stuck. The only way to try that now would be to rescan the negative. Bummer.
So when you have original negatives to work with, get the best quality scan you can and save them in a non-distructive format, and never change those pixels.
hope this helps.
AdChoices