Hi Serra,
you can use any non-fluorescent media for mounting, except for anti-fade reagents which prevent the photobleaching of the acceptor dye. When we use formaldehyde for fixation at the end of the experiment, we leave it on the cells, otherwise, we use PBS or glycerol, or 1:1 PBS:glycerol.
If you need an efficient software for the analysis of your images, I recommend our free ImageJ plugin:
<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.biophys.dote.hu/accpbfret/" target="_blank">http://www.biophys.dote.hu/accpbfret/
Best regards,
Janos