Tournament Scheduler does not have an option to set to force teams not to play one another, but you are able to manually seed teams into the event to insure they do not play.

For Bracket Events...
After creating the bracket event, you can click on a bracket position to pick the teams or if your team list is displayed, drag the team to a spot on the bracket. Set each team on a different half of the bracket.

For Pool Play Events...
After creating the pool play event, click on one of the Pool tabs and then click on one of the matchups and pick one of the teams. Then click on a different Pool tab and choose the other team.

You can then randomly seed the rest of the teams into the event by clicking the seed button.