The most efficient way to make cd() more efficient is to not use cd() at all. There is never any need to use cd() in matlab code and it's actually a dangerous thing to do (if you cd() into a directory that has a sum.m file, you'll suddenly be using that function instead of matlab own sum and when you cd out of it again, you'll revert back to the normal sum).
All of matlab functions that deal with files (such as load, xlsread, fopen, etc.) can read files whereever they are without needing to change the current directory. So, instead of
cd(somewhere);
data = load(somefile);
you use
data = load(fullfile(somewhere, somefile));
This will be faster as well.
To build the path out of several bits, as Walter said, use fullfile. You don't even need to write the directory separator ('\' or '/'), fullfile will use the correct one for your OS. As for building the folder name, you can use concatenation [], or sprintf, so:
folder = [site, '_', layering, '_reports'];
fullpath = fullfile('F:\SCG_JW_3\JacksonWilsonWest3PostInversion', date, folder);
data = load(fullpath, 'somefile')
or using sprintf which I find cleaner:
folder = sprintf('site_%s_reports', layering);
fullpath = fullfile('F:\SCG_JW_3\JacksonWilsonWest3PostInversion', date, folder);
data = load(fullpath, 'somefile')
