Only a TT User who is also a Salesforce User can Check-In to Jobs within Salesforce.
Please create Salesforce User and then create the mobile Time Tracker User ID's. While creating Mobile Users, please link Salesforce User ID with the Mobile user. Only then the Salesforce user has an option to Check-In for a Job within Salesforce.
Link TT User ID with Salesforce User ID
When the TT User Logs in to Salesforce and clicks the Time Tracker Tile they see all Mobile Time Tracker related Tabs with a button at the bottom of the Salesforce screen as "Track Time". Using the Track Time button Salesforce User can Check-in/Out for Jobs within Salesforce.
Please note that there is no Clock-In/Out button to track time within Salesforce, you see only Check-In and Check-Out buttons for tracking time.