Start by putting them in a towel lined, sheltered structure of some kind (box, kennel... Etc.), but leaving them where they are for now. Once she accepts that, you can progressively move it closer and closer to where you want it be. If at any point she starts to take them out and move them... Return the "nest" to the last place she felt comfortable and wait a little longer. Generally if she sees what you're doing as an improvement, and has a basic trust of you, she'll go along with the change... But it will depend on just how feral she is. If she'll come to you when you have food, or let you watch her while she eats, your chances are good.
Kittens eyes don't open until 5-8 days, so that's nothing to worry about it's just because they're so young.
Whether she's your cat or not, once the kittens are weaned, you'll need to see that she gets spayed, otherwise this will repeat itself very regularly. There are always local organizations that can help with spaying fees in such a situation if necessary. Look in your local paper under "pets" and call the different adoption agencies for help and advice.