You don't want to squish bees and with a mite wipe you don't want to poke holes in it's fragile wrapping.
Here's the beekeeper recommended way of clearing space on your top bars to add a treatment.
Smoke to move the bees off the top bars and push them down and out of the way so they won't get crushed.
A ton of smoke isn't needed. Pause between puffs to give them a moment to move.
Hold it low down, not quite flat, and slide it along the length of the bar. The combs will ride up on the hive tool.
If bees are on it they can surf on the combs.
You may find it easier to smoke an area and do it and then smoke the next area as the bees tend to come back quickly when honey is exposed.
Place the scraped off combs on the front porch for the bees to eat. Don't let them go to waste. The bees will recycle the honey back into the hive and sometimes some of the wax too.
The leftover wax can be collected later to be used for candle making.
Nothing is wasted.
In this case I'm adding a single Mite Wipe.
Other treatments or product that could be laid on the bars are pollen patties, AFB powder on wax paper, sugar syrup in a plastic baggie.
The same cleaning methods are used for all these products.
Are there tons of bees on the bottom of the box or a large build up of comb hanging down?
Combs could puncture the wrapping on a mite wipe when the boxes are placed back together.
Smoke the bottom of the box to move the bees up inside out of the way.
Scrape if necessary, however most of the time scraping the bottom box is sufficient.
Set the box into position on the treated box and you're done.