Can I handle two separate companies under under same Freshdesk account?

Yes, you can do this in Freshdesk. You can make use of the Multiple Products feature where you can have separate portals for the different companies and also have different groups and emails for them as well. To know more about the setup you can check out the article https://support.freshdesk.com/support/solutions/articles/37638. If you are not in the Estate or Forest plan you can still setup different support email addresses and groups for the different companies you support.