The boxes will need to be removed completely. You can modify the side covers by cutting them to fit, but depending on the size of the filter, they may still not work. And the clearance with the battery box, as 5twins stated.
They are held on with clamps.
But not all pods are the same. Some have a lip inside on the rubber throat that will block the air ports on the carbs. Mainly the BS carbs.
And yes, your carbs will need to be rejetted. More air coming in will cause a lean condition, so you'll have to get larger jets.