Spatial resolutions in optical microscopy
The theoretical resolution for an optical microscope depends on the wavelength used, but is close to 0.22 um (220 nm). Confocal microscopy does not greatly improve axial resolution; it dramatically improves the in-plane resolution (x and y directions, by excluding extraneous light). Theres not a lot to do to "cope" with that using those techniques. If you need more resolution, you can use the super-resolution techniques you mention, or the good old TEM.

There is some more information on the Nikon website: http://www.microscopyu.com/articles/formulas/formulasresolution.html 

and on Olympus website: http://www.olympusconfocal.com/theory/resolutionintro.html