If like me, you have three reefing points on your mainsail you’ll have a lot of spare rope to deal with when flaking the sail. There are a couple of ways to deal with this. You can flake the sail and then pull your reefing lines through but this has two disadvantages. Firstly it means you will have more rope in the cockpit (or at the mast) but worst is when you come to hoist the mainsail and those coiled ropes inevitably get tangled or caught on something as they run through the blocks. There is a lot of friction, even with the most free running reefing lines so it takes much more effort to hoist the mainsail.
A simpler solution all around is not to pull the reefing lines through at all when you have flaked the mainsail. Instead, starting from the back, gather and lay the lines on top of the furled sail and tie them down using the tails of the sail ties. This is very fast to do and makes hoisting the mainsail the next time much easier and faster. One small disadvantage of this system is that if you have not tied up the reefing lines properly, they can drop off the top of the sail and poke out the bottom of the sail cover in the gaps between the fasteners.
A solution to this is to modify the mainsail cover so that it does up with a zip. This continuous closure stops any reefing lines from dropping out. The zip starts at the back and goes as far as the vang. A zip is a very simple and effective way of fastening a mainsail cover. There is a gap at both ends to ensure a good flow of air through the cover. The zip is protected from the sun so should last for many years.