Having a reference skip a Level in your workflow requires modifying some Form and Level Settings and Filters.
In Manage Levels, open the Level Settings for the Level to be skipped. For the option "References Can Skip This Level," select "Yes, references that are not assigned to any mandatory forms can go to the next level."
Open the Form Settings for the Form in the same Level. For the option "Optional Form," select "No." Then, a Filter must be created in the Form Settings to "catch" the references that will not be skipping the Level. You can build a Filter to move references based on their RefID, a specific answer, label, or filter for a specific % of total references.
As an example, if you want all the references except those with RefIDs 1-50 to skip the Level, you would click Add Filter and select the "RefID Range Filter" option, and enter the range 1-50 into the text field.