Doesn't do the boat any harm to deflate it and store. Used to do the same with a Zodiac Mk II CGT for 15 years!
Remove the engine. Good opportunity to get it serviced, winterised, etc. With the engine off, wash the boat with a mild detergent, remove the floor (whether aluminium or ply) and rinse well. Importantly, ensure the boat is thoroughly dry. Remove the valves and allow the boat to deflate. With the air out of the boat, fold the cones ends in one on top of the other on top of the transom. Pull the sponsons or tubes in so they meet in the middle (you can use the rope lace cuff to do this). Starting at the transom roll the boat towards the bow (bit like swiss rol!) The boat can be tied with a rope to keep it in that shape.
Store in a well ventilated and dry garage. Any danger of rodents, then consider lifting off the ground, etc.
All the ancillary equipment such as valves can be cleaned and greased, oars varnished, etc.