It sounds like you've defined one data source table for both Treatment notes and Impairment Rating Notes.
A few general facts that may help you:
You can delete any field from any layout where you don't want it simply by entering layout mode, clicking on the field and pressing the delete key. This change will not affect any other layouts in your database file. If this is a table view layout, you can click the modify button and clear the checkbox next to the field to hide it from the table view.
In Edit | Preferences on the Layout tab, there's a preference setting: "Always add newly defined fields to current layout" that I think you may have selected. I find this to be an annoying feature as it frequently results in undesirable modifications of my layout design and I keep this check box cleared so that it doesn't happen.
Should you have both impairment notes and treatment notes in the same table or in different tables? There's no hard and fast rule to enable you to choose one over the other. There are trade offs either way and you have to analyze what you need the database to do for the user and choose the design that works best for you.
What would be the disadvantage for having separate databases for these two types of notes?
It all comes down to how you need to use the data. Please note that I've talked in terms of separate tables, not databases. Both tables can be maintained in the same file and this will likely be easier for you to work with.
If all this data is one table, you can more easily create a report listing multiple records of both types of data in the same layout. On the other hand, if the fields needed for both types of records are very different, you could end up defining a large number of fields with only a portion actually used for any given record. This can result in a complex table definition that is harder to work with. In which case, it may make more sense to define separate tables and link both to a parent record such as an "office visit" record and/or a patient record.