Ok as a qualified fitness instructor as well as martial artist I hold courses on physical fitness instruction for all of our Instructors - the basic structure of which is:-
Pulse Raiser/Mobility - Gradually increasing the heart rate and core temperature of the body through low impact progressive continuous movements involving large muscle groups thereby getting the flow flowing to the muscles. Getting the joints moving gently increasing the synovial fluid which will avoid any injuries later on.
Couple of Maintenance Stretches 6 - 10 seconds for quads, hamstrings, deltoids, Pecs etc.
Sustained cardio - utilising high impact aerobic exercise to improve cardiovascular endurance for a good 15 minutes
Cool Down - Bringing the heart rate back down gradually and reversing the cardiovascular build-up, progressively reducing the impact from high to low to avoid blood pooling i.e suddenly stopping cardio work and the blood rushing into the open blood vessels of your lower body's active muscles and less blood being pumped to the brain thereby causing dizziness/fainting.
Muscle Strength Work - working Abs, Adductors, Abductors, Hamstrings, Erector Spinae etc i.e sit ups, push ups, etc.
Finally Flexibility - Stretching - depending upon time at least short maintenance stretches of all the muscles worked in the Muscle Strength Work section as well as a couple of Developmental Stretches to improve upon present range of movement.
I have found that using the above as a guide our Instructors are able to provide a good overall workout for students incorporating their martial arts training. I would certainly always ensure that at the very least your core temperature is raised prior to executing any stretching technique. If you look at your training regime you will be able to write your own work-out using the above as a basic guideline to safe exercise practice.
Hope this helps a little - I'm new to Martial Talk so this is only my second attempt at throwing in my two pennies worth
