You can try: 1) methylene blue to distinquish dead and alive cells of fungus and root.

or 2) Gram staining procedure too see the dark blue fungal cells.

I use the GFP inserted in trichoderma and it clearly appear when you see under the fluorescence microscope 

I think you can try Ink and Vinegar. 

Vierheilig, et al. "Ink and vinegar, a simple staining technique for arbuscular-ycorrhizal fungi." Applied and environmental microbiology 64.12 (1998): 5004-5007.

wheat germ agglutinin (WGA) staining