In Perusall, each assignment must be derived from a single document (or part of a document -- you can create an assignment from a page range or based on the table of contents). However, if you want multiple assignments to be logically grouped together, set each assignment to have the same deadline. Then Perusall will group those assignments together in the Assignments panel on your course home page.
If you want, you can also adjust the number of annotations Perusall will score for each assignment by editing the settings for each assignment. For example, if you normally score the top 10 annotations in one reading assignment per week but need to create two reading assignments in a particular week, you can tell Perusall to grade the top 5 annotations from the first assignment and the top 5 from the second assignment, overriding your course default of 10.