Good Morning all. I have a two part question and REALLY dont know what to do. I live in Nebraska and am new to beekeeping. I received a package of bees back in April with all brand new equipment. Since then I have added a second brood box and as of last month added a honey super, which is currently about half built out with drawn comb and honey. My bees are thriving in my estimation. My questions are this…I want to treat for mites this fall AND want to leave the super on all winter for food for the colony. However, I would like to harvest two frames for myself. I am getting advice saying don’t leave your honey super on all winter and other people say DO leave it on for food for the bees. What do I do?? My second questions is when I treat for mites using Apivar, the directions say to remove the super to not contaminate the honey for human consumption. Is this correct and what do I do with the bees in the honey super? The super seems to be very populated with bees. Should I use powdered sugar to treat for mites and then I can still harvest the honey and not remove the super? Sorry if this is long winded. I just dont understand how a person can remove a super full of bees to treat using Apivar to not taint the honey. Thanks for any advice.
The powdered sugar is to test if you have mites and how many are in the hive, it isn’t a treatment to eradicate them Brian. I’ll leave the rest to those that know more about Varroa as it isn’t in Australia yet.
Cheers
Thank you Peter. I appreciate the response.
You should pull the frames you want before you treat if you are going to leave the super on for the winter. In your area your local beekeeper group is probably a more reliable source for deciding to over winter with the super on or off-- if you are single brood box I would think they would need that super without the queen excluder on to overwinter in your area but I’m near Detroit and don’t have the exact same climate as you but do have pretty brutal winters snow and temp wise.
If you are single brood box and you have at least 3 frames of honey like I typically have in my brood box and I am able to overwinter as a single brood box without a super without a discernible loss due to starvation-- usually its mites related. I do use Oxalic Acid (Provap vapour delivery) and Apivar strips and it is very effective for my 21 hives.
If it is a Flow super, I highly recommend that you take it off over winter. If you don’t they will likely coat it with propolis, which will make extraction very difficult next year.
If you have 2 brood boxes, they can likely manage without the super. You may need to feed them a bit, but that is normal for a northern climate.
You absolutely must do that with Apivar. If you really have to leave the super on, you could consider a formic acid treatment, like MAQS (Mite Away Quick Strips). I believe the only other treatment that is safe with a super is thymol. I wouldn’t use it though, because it is not very effective, and it can scent the honey. By the end of this month, your colony will probably have shrunk enough to shake the bees out of the super and remove it. If I am doing Apivar, I usually do it in early September, after I have removed the super. The rest of the year, I use Oxalic Acid vapor. As that treatment only takes about 15 minutes, I just take the super off while I treat, then put it back right away.
Some people advocate powdered sugar as an organic mite treatment. However, proper research does not confirm that it is effective. As @Peter48 said, I use it for doing mite counts, but I never use it for treating.
If you want a really good guide to what treatments are available and how to use them, this is a great start. It is a bit out of date on Oxalic Acid, but it will help you understand the recommended methods:
I am happy that you are considering treating for varroa. Well done. 
I actually have two brood boxes with a super on top. My equipment is a langstroth. I’m sorry, I should have been more specific.
Thanks for that clarification Brian. Dawn has given you the best guidance here. She is spot on.
Thank you Dawn for all the great advice. I want to give my colony the best opportunity to survive the winter. Just wasn’t sure how to deal with starvation and mite control. What is a good food source for my bees over the winter that I can provide for them?
Until your night-time temperatures consistently get below 55°F, you can feed them sugar syrup. I use 5 parts sugar to 3 parts water. Once it is cold overnight, they will probably stop taking it, as they can’t dehydrate it enough for storage. At that point you can switch to candy, or even pure white granulated sugar. Depending on the stores they already have, you may not need to feed at all. Don’t give them patties with pollen substitute (or protein) before late February. If you do, you may stimulate a population increase, and they won’t have enough food for all of the new bees.
I agree with everything apart from a short comment on thymol.
Thymol (apiguard) is an effective varroa treatment but you must remove the supers as otherwise you will have thymol flavoured honey. Thymol needs average ambient temperatures of around 15C to be effective, and as the thymol must stay in the hive for 28 days, there is a norrow window for treatment - after the removal of the supers and before the weather cools. Against that, it is very safe, not harmful to queen or brood. It is also, like formic and oxalic acids, classed as organic, but has none of the handling issues that these do. And unlike apivar it has no reistance worries as resistance has not been seen and is considered highly unlikely to develop.
My standard varroa treatment regime is thymol in August and oxalic acid in December.
Jim, I’m curious about your December Oxalic treatment-- we usually have snow here in Ontario Canada in December and I wouldn’t have thought to do an oxalic treatment at that time; do you have snow in Ireland when you are treating? If not, are your bees buzzing about in that time of year?
The manufacturers of the Varrox OAV iron are Swiss. Their instruction video says that whenever the temperature is 4°C or greater, you can treat. 
Gotcha. I just wondered because usually when I treat in the fall after I reopen the entrances bees pour out to cool off so in snowy weather I wondered what happens to the bees-- do the pour out and then freeze or do they stay inside despite the increase in temp and break torpor?
I haven’t done it myself, but they seemed to stay inside in the hive that Varrox showed in their video. If you think about it, although the iron reaches around 400, the sublimation temperature of oxalic acid is 157°C. Unless under pressure, the vapour cannot get hotter than this. If you hold your hand 5cm above a steaming mug of coffee, it doesn’t feel very warm, although the drink may be at 60-80°C. I would imagine that the same is true of OAV in a hive, as the cluster is likely to be at least 10cm or more above the hot iron. Just theory on my part, I have no direct experience, but I am sure that @JimM will chime in.
Tim, it’s much milder here. While we can get snow it usually disappears in a couple of days. The typical December daytime temperature would be from 5-12C so there is usually no problem to treat on a mild day.
In past years I have used the dribble method (5ml between each frame of bees), but this year I will be using a gasvap.
And yes, bees will be flying here on mild calm days in December, mostly cleansing flights but sometimes they will even bring in pollen. We get a lot of rain which is tougher on the bees than cold. Mild winters can result in stores being used up causing starvation in early spring if we are not careful.