To get HRU output, uncheck the "limit HRU output" box before running the model. After running the model, select "Read SWAT Output" to read selected output files into an Access database (scenarios/default/tablesout). Using queries in Access is MUCH easier than manipulating the text files, generally speaking.
As for changing CN2 values, I tend to do it in the mgt1 table for selected HRUs (or for all of them if I'm doing initial calibration to get things in the right range). I would generally not change the database values, though I do see that ArcSWAT seems to give you that option. I don't know why that doesn't work -- but in any case I'd make copies of the original databases for use with future models before altering any values.
-- Jim