Just add the additional amount to the quarterly estimates you already make through QuickBooks.
You won't be penalized for paying too much, you'll just get a bigger refund at the end of the year.
To estimate the amount you owe for the second business, you calculate your quarterly net income (income minus expenses) and then multiply that by a percentage equal to your (Income Tax rate + SE Tax rate - (Income Tax rate x SE Tax rate x .5) ). So, if you are in the 12% tax bracket, your percentage would be approximately (12 + 15.3 - (.12 x .153 x .5) = 26.4%). That little subtraction in the formula is because you get to deduct as an adjustment to income half of your SE tax.
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