First, check the microscope's specifications to make sure it is properly configured. Things to consider:
IRDye 800CW: Several filter sets have reportedly been used successfully to image this dye.
IRDye® 800 Infrared Dye Filter Set: Chroma Technology Catalog #41037
Exciter HQ740/35x Dichroic 770DCXR Emitter HQ780LP 2
IRDye 800CW Custom Filter Set: composed of three individual filters from Chroma Technology
Exciter HQ760/40x Dichroic 790DCXR Emitter HQ830/50m
Cy® 7 Standard Filter Set: Chroma Technology Catalog #41009
Exciter HQ710/75x
Dichroic Q750LP
Emitter HQ810/90m
Set number 2 appears to be the best spectral match, but the other sets are acceptable substitutes.
IRDye 680: For imaging of these dyes, the standard Cy5.5 filter set stocked by Chroma Technology is a good spectral match.
Cy® 5.5 (Red Shifted) Standard Filter Set: Chroma Technology Catalog #41022
Exciter HQ665/45x
Dichroic Q695LP
Emitter HQ725/50m
You cannot see near-infrared light when you look through the microscope oculars — it is not visible to the eye. Use a DNA stain such as DAPI or Sytox Green, or co-stain with a visible fluorophore such as Cy3, so you can easily locate cells and focus on them. Then, switch to the NIR channel and use the CCD camera and computer monitor to visualize the NIR image in pseudocolor.