My understanding is that I can take out $100K from my IRA without penalty because of the Care Act. The question is do I need pay the taxes all now or over 3 yrs?

Yes you can spread the taxes evenly over 3 tax years  and if you do end up repaying some or all of the distribution amended returns will be required. 

IF you can certify you suffered a COVID-related hardship, you can withdraw up to $100,000 without the early withdrawal penalty.  You can choose the spread the income and tax out over three years, and you have three years to return the money.  If you return part or all of the money before the 3 years are up, you will need to file amended returns for any previous years.  Make sure any returned amounts are reported as such to the plan trustee before you send the money, so they don't mistake it as a regular contribution.