Definitely harnesses are better for when you start walking them.
None of my dogs wear collars in the house - I'll tell you why. When dogs play together and are rough - they can get themselves caught up. One of my friends who is a vet nurse, went upstairs (above surgery) at lunchtime to find her two springers caught together. One had it's jaw under the other one's collar, they had twisted round - and one was unconscious - the other had a damaged jaw. Because she lives above the surgery, she was able to get immediate vet attention and they revived her dog that was unconscious - the other was very very bruised......
I'm really glad you've taken their chains off - now you'll probably take their collars off too

(and unsupervised tbh I would definitely do that, esp with two pups). As long as your garden is really secure they'll be fine in the house and garden with no collars on.
You can start practising their recall in the house and garden now too, every time you feed them you can blow a whistle - with two dogs, whistle training is much easier - all 5 of mine come to the whistle - we have individual whistle toots and a collective one