In the event that certain line items need to be hidden from the Order Schedule output, you can use the Hide Line functionality for both Standard and Bundled Line Items.
Bundled Items can inherit the value from a Bundle, but non-bundled Quote Line Items must be updated by a user, or through a workflow.
Quote lines utilize a field called "Hide on Quote" (API Name: tysoxrr__Hide_on_Quote__c) to hide lines from the output.
To Hide Lines, simply check the "Hide On Quote" box on the Quote Line Item, and that line will not be displayed on the PDF output. Note that any $ Values associated with it will still calculate.