This stuff works GREAT. We've used it as soon as we realized what happened. Not sure how well it works if it's been awhile since the skunking:
https://www.amazon.com/Skunk-Odor-Destroying-Shampoo-Greasers/dp/B0002DIOE4
Happens to the best of us, my dog got sprayed too once...good thing I don't think it was directly otherwise the smell would have been worse.
For the house, open the windows and if you can stand the cold, leave fans/AC on so the air can circulate. Otherwise you can try spraying Febreze or other air fresheners to try to get rid of the smell but they ain't that effective, to be honest.
For your pup, I'd give her a bath. I got this from Amazon and it works wonders: https://www.amazon.com/Skunk-Odor-Destroying-Shampoo-Greasers/dp/B0002DIOE4/ as for her eyes since you rinsed it thoroughly, I'd consult your vet to see if eye drops/eye wash can help.
Good luck.