There are no subjective philosophies about which parameters to adjust and by how much.
My general rule of thumb is to leave parameters based on measured or observed data alone as much as possible. This includes things like slopes, and soils data. In particular, the SSURGO data is pretty detailed and I'm generally impressed with the care soil scientists take in describing soil. (The STATSGO data lumped many units together, some of which were quite different, so changing parameters could be easily justified.)
So I tend to start with parameters that are not measured easily or at all -- like esco, and gw_delay.
And some parameters can start with ArcSWAT-suggested default values, based on real observations, but can still be quantified only approximately -- I'm thinking of curve numbers in particular here. Although they were originally conceived to be watershed-scale parameters, they have been quantified at plot scales in order to estimate their values for different crops (as I understand it), and this is how SWAT uses them. But we apply curve numbers at HRU to subbasin scales that are much larger than plots, and so changing curve numbers as needed makes sense to me -- they are not rigid values and somewhat scale dependent (and rainstorm-duration dependent -- Paul McGinley had a paper on this).
On the other hand -- even detailed data like SSURGO are not perfect and uniform, and if needed I'll modify those values as well. It's just not my first choice. I don't know if changing all layers, or just the top layer, is better / worse. I tend to change all layers (at least the top 3) if it's a parent material property. If it's an A-horizon property (organic matter, and perhaps AWC based on organic matter?), then I guess just the top. You're right that the literature is a bit lazy in reporting what was actually done.
Good question.
-- Jim