Hi! Welcome to DT from Colorado!!
Of course, all I have to go on is what you've said and looking at your picture, but as far as I can tell, everything is normal for you guys.
It is OK to take off the cone; you can just let her ears dangle. Or you can tape them tip to tip over the top of her head if you'd like...just don't put any tape across an open cut area.
I think I would leave the cotton in place if it is just ordinary cotton or gauze---so long as there is no adhesive, latex or other non-breathable material in it. But if it is just loose wadding, I would think it would be OK; I would hesitate to pull it off if it is stuck to the stitches because I wouldn't want to pull off any scabs she's got going. I would probably peel off what I could to make the wadding thinner, but again, try my hardest not to disturb any scabs. It's really best to leave them alone and let them heal on their own; you don't even have to put any ointment or antibiotic spray, etc on them.
Keep an eye on it though...if you start seeing goopy stuff like a stinky discharge, or red irritated-looking swelling, she could be developing an infection and might need a vet visit if you don't see improvement within a day or so.
To a limited extent, it's even OK for her to rub her ears or scratch at them a bit, so long as you're not seeing any real damage to the stitched area. Usually when a puppy does that, she'll quickly learn it HURTS if she messes with it, and she'll leave it alone.
Check out this thread for a bit of info about handling newly cropped ears: https://www.dobermantalk.com/ear-cro...-s-don-ts.html
There are also a couple of threads referenced at the bottom of that first post you might want to glance at. You're not ready to start posting at all--her stitches need to be out and her ears healed with no scabs or open areas (usually by about 6 or 7 days after the stitches are removed), but you can at least familiarize yourself with the posting method we recommend and start to lay in your supplies.
Again, welcome to DT. I love your pictures--they're both cute-looking little people. Stick around, ask questions, tell stories (especially the naughty puppy ones--misery loves company and we've all been there before). AND post more pictures.