Remove the red rubber insert to gain access to all five holes.
Which filters are you referring to? According to Keurig, their 'My K-Cup Universal' fits all of their coffee makers. At least it does my Supreme.
It has a mesh filter, so I don't use a paper insert. Cleaning it is as simple as emptying then rinsing. It does eventually get a small build up of oils at the bottom mesh supports, but a scotch-brite sponge removes most of it. As for any that might remain it's really a cosmetic thing and doesn't affect taste.
Honestly I would think that a paper filter would somewhat limit the amount of coffee the filter would hold, but I've never tried one.
If you do go with the universal, read the instructions. There are complaints that it doesn't fit because users forget to remove the existing pod holder or don't remove the gray plastic extender, which is meant for 2.0 machines.