I thought I'd go in and take one of the supers off and have my first go at honey extraction but I found that only half the cells on each frame are capped although all contain honey. How long should I wait until I can be sure all the cells are capped?
Also, my bee books say to remove all the supers in August, should I not leave one in each hive for winter food? I heard that if I do, I should put them under the brood box, is this correct?
As it's 2017 and honey refractometers are readily available, give accurate indications and can be bought for very little money (mine was less than £15) I strongly recommend you to buy one from Ebay. You can readily check the honey water content with that.
The all supers off in August doesn't fit all circumstances or locations, however if you are using autumn thymol based treatment and you don't take hives to the heather it's a useful guide.
There will most likely be some stores in the brood box but if you remove all the supers containing ripe honey and extract it (some do, some don't) you need to ensure the colony has adequate stores to overwinter. Straight sugar syrup without any marketing hype works perfectly fine but adding some Hivemakers recipe to stop fermentation is to be recommended. There's also late natural forage such as ivy.
During winter in a natural (feral) hive bees would have stores above their cluster and the cluster would move upwards as the food is consumed. If you leave a super on top of the brood box take out the queen excluder or the bees may move up to follow the stores, leaving the queen trapped under the excluder to perish.
Be aware that removing the excluder in this manner will, in spring, yield a colony in the top of the hive (the super) and the queen will start to lay eggs up there so you will have brood in your super. (not the end of the world but some people are squeamish about honey from brood cells)
By Nadiring the super in Autumn the bees will move honey up into available space in the brood box where it is closer and warmer. The nadired super box may initially hold excess stores but it will be emptied first. By leaving it on it forms a natural wind break, stopping eddy currents of cold air.
Remove it in a timely manner in the spring or an expanding brood nest may intrude into your super comb. Erichalfbee has suggested taking the nadired box away after a few weeks which will preserve the comb but loses the windbreak effect.
As with all things bee there's more than one way to skin a cat.