Your choice of either the 'raw data' or 'distance' approach will determine what kind of inferences you can make about your data. If the latter is chosen, interpretations along the lines of 'how different are sites X and Y" are appropriate. Perhaps most importantly, by using a distance matrix you create dependency among your data values. Thus, any statistical method that assumes independent trials will not be appropriate.
Would you like to explore relationships in your...
...raw data