One excellent way to combat differential charging effects is to electrically isolate (or "float") the entire sample from the specimen holder. This "specimen isolation" technique is similar to that used in secondary ion mass spectrometry  and effectively makes the entire sample (both insulating, semi-conductive and conductive areas) behave non-conductively. Methods employed with good success here at Surface Science Western include mounting samples on non-conductive double sided tape or mounting on glass slides.
Figure 1. Differential charging issues can be caused by both insulating to semi-conductive island structures (top) or by layered systems (bottom).
 M.A. Kelly, Analysing Insulators with XPS and AES, in: D. Briggs, J.T. Grant (Eds.) Surface Analysis by Auger and X-ray Photoelectron Spectroscopy, IM Publications, Chichester, 2003, pp. 191-210.
 J.B. Metson, G.M. Bancroft, N.S. McIntyre, W.J. Chauvin, Surf. Interface Anal. 5 (1983) 181-185.