To separate teams you can simply create extra accounts with (slightly) different names or added numbers.For example: company-hr.signrequest.com and company-sales.signrequest.com.
By clicking in the upper right corner you can select your team and define which branding your signers will see and determines where the documents will be stored.
For each team you can invite team members. These members will only view the documents of the team they are a member of and not the documents in other team accounts or your personal (private) account.
You can make as many teams as you want and use different color's and logo's.