Can i use ITIN Number to issue 1099 Misc?

Yes, you can. 

Enter the payer's or recipient's taxpayer identification number using hyphens in the proper format. SSNs, ITINs, and ATINs should be in the XXX-XX-XXXX format. --https://www.irs.gov/pub/irs-pdf/i1099msc.pdf

When adding the information for an ITIN for a contractor under Quickbooks online, am I putting it under the individual section and under SS# or changing the formatted numbers and putting it under tax id #?

Under SSN.

Social Security Number.