You can create a saved search designed to catch only the text of the smaller bill you're tracking.
When a smaller bill that you are tracking is rolled into an omnibus bill you will need to begin tracking the omnibus bill separately in order to continue monitoring the status of that bill.
To ensure that you're notified when a smaller bill has been rolled into an omnibus bill, set up a saved search using key terms from the bill. If you set up saved search alerts, you'll then receive an email notification when a new bill that includes the text of your smaller bill has been introduced or amended.
Once you have identified the omnibus bill, you can then track the specific omnibus bill to continue monitoring the smaller bill that has been rolled into the omnibus bill.
Example Scenario
If you were tracking MN HF 4083 about freedom of expression for student journalists, you could set a saved search for the first line of bill text "[121A.80] STUDENT JOURNALISM; STUDENT EXPRESSION." The search for this exact phrase currently yields only four results and would notify you when the education omnibus (MN SF 3567/MN HF 3782) was introduced with this language.