Cognitive Flexibility Theory does not outline specific methods of instruction as many other ID theories do.  There are several principles that instructional designers should keep in mind as they use other cognitive theories for designing instruction.
Learning domains must provide multiple representations, explanations, and examples of instructional material so that learners can construct information representations.    
Instruction for mastery of complexity and application should reflect the conceptual interrelatedness and interconnectedness of ideas in complex knowledge domains.  
Instructional materials should focus on knowledge construction rather than transmission of information.  
Instruction should support context-specific knowledge and avoid oversimplification, compartmentalization and/or linearity of content.  
Instruction should include practical, real-world contexts to allow transfer of basic concepts and theories to be applied in dynamic situations.