There are certainly books one could read, but its best to just try some
experiments to see if the technique will work for you. If you decide to
become rigorous in trying to extract information from the technique I'd
suggest reading "Principles of Fluorescence Spectroscopy" by Joseph R.
The major concern in choosing a pair probes is the distance range you
expect to measure. Basically, the degree overlap between the donor
emission and the acceptor absorbance sets the range over which transfer
will occur. If you know anything about the protein size or structure
you can get a handle about what distance range to start with. I'd
suggest you track down the catalog from Molecular Probes Inc.
<http://www.probes.com/> Their print catalogue probably has enough info
to start doing preliminary trials. You also need to figure out a
labelling strategy (e.g. specific vs. non-specific, cysteine vs.
Best of luck