You're experiencing 2 very common things. Alot of horses stock up for one reason or another. 99.9% of the time the stocking up will go down with turn out or exercise. As you can already see that if you take him out on long rides, no stocking up, short rides (=less exercise) he'll stock up. Maybe if you lunge him for a while before taking him out on short rides he'll be less likely to stock up on ya.

As for the windpuffs. Those will not go away. They normally happen after a horse has experienced some sort of stress in that area. Maybe from a ride where he might have stepped funny or made quick turn or even just playing out in a pasture. They are nothing to worry about as long as its not accompanied with lameness or soreness.

From the Merck Veterinary Manual: These puffy, fluid-filled swellings around the fetlock joints (of either or both fore- and hindlimbs) usually are not accompanied by heat, pain, or lameness. They are said to be associated with trauma and hard exercise, but the exact pathogenesis is uncertain. Although usually benign, windgalls should be regarded with suspicion in the presence of lameness. Some horses, particularly heavy ones, seem to be more susceptible. Treatment is problematic; in the absence of lameness, it is unwarranted. Windgalls may disappear spontaneously or respond to periods of rest, bandaging, and exercise. Recurrence is common.

If he's stocking up the more turnout the better and 24/7 if possible.  Make sure the water and the hay are far away from each other and a turnout buddy to make sure he moves around as much as possible.  Supplements like daily MSM or aspirin can help also as they target inflammation.  I would not wrap for stocking up unless you were showing the next day or it was severe.  As long as he's not lame I wouldn't worry too much about it.  It's very common

Windpuffs can also be helped with MSM.  I always buy a good quality MSM made in the USA. 

http://www.su-perstore.com/m7/sfemsmultrapure--su-per-msm-ultra-pure-powder.html?bcsi_scan_a7df3166a227563b=PIMo4T+RlBweBJZ94GM1xsISnX0vAAAAe0okBg==&bcsi_scan_filename=sfemsmultrapure--su-per-msm-ultra-pure-powder.html

A lot of water is needed to manufacture it and if it comes from China, their water quality is very poor.  You can also sweat windpuffs to bring down inflammation.

I agree with the others regarding stocking up; it is common and will improve with exercise.  My gelding is prone to stocking up.  Just simply standing on the packed dirt floor of the barn for a few hours will cause his hind legs to get puffy.  If you stall your horse, deeper bedding should help; but the best solution is 24/7 turnout, as the others said.