I extracted some honey yesterday but the frames still feel quite heavy ( maybe there is some residue rape seed, although I did extract after the rape harvest). I am going to put them back onto the hives for the bees to clean and use for their winter stores. Do I put them above or below the queen excluder or do I now remove the queen excluder completely? Is there a chance the queen could lay in these supers?
There are two schools of thought.
1/ Put the box to be scavenged under the brood box. ("Nadir" rather than "super".) Remove it either in a week or two, or around the beginning of March. No QX. The bees should move the honey from the 'wet' frames up into their 'proper' store before the winter.
Don't put lots of boxes under at the same time - that makes it hard for the bees to defend the entrance against robbers.
2/ Put it above the brood, but in such a way that the bees think it is outside their home - so that they will rob it out. (This can start robbing from other hives in the apiary, so its best to be given in the evening.)
You convince them its 'outside' their home by only allowing access through a small hole - like a ¾ blocked Porter escape hole (a scrap of plywood or such can be used as the restrictor). And you can further the impression of 'outside-ness' by putting a totally empty shallow box between the small-hole-coverboard and the box with the wet frames. Again the QX has no part to play, and should be removed, cleaned, and stored away for the winter.
The boxes are removed once the bees lose interest in them - and then they should be treated before storing away.
Some folks do just store them "wet", believing it deters wax moth. It doesn't deter the Lesser Wax Moth …
Whichever route you choose, I'd strongly suggest reducing the hive entrance with the reducer block AND then stuffing in a bit of sponge to really close it down - preventing robbing is easier than stopping it!