You can totally do this.
Multiple teams & channels support
Check-ins allow you to setup the daily check-ins for each of your teams.
A team cannot have more than one daily check-in configured, so in order to achieve this you should create different teams.
Once you have created the Team, please activate Check-ins for that team by going to Check-ins > Manage Check-ins and then opening the preferences for the team you are configuring, there you can specify the channel/room where you want the reports to be posted.