Ok, while there are MANY ways to do so, let me suggest you some simplest:
First “diff” supposed to differentiate between files, so you may wish dump the output of the directories in the files first:

Like “ls -1 > file1” in one directory and “ls -1 > file2” in another directory. Option “-1” instructs ls to format output one name per line as it will make it more convenient for our use. So then you can use “diff file1 file2”.
As you want to compare the content of the files in the directories, the simplest is to dump the files from the first directory into one file and files from another directory into another.
To do so you can use command “xargs” as it creates list of parameters: “cat file1 | xargs cat > filedir1” . You can use < instead of the first “cat” in the line. You then do the same with a second file you have created and then you can run diff for these two new files and account for a differences in file content. I hope it is what you have been asking for.
Get “UNIX in 24 hours” or “UNIX Essentials and UNIX Core” DVD if you have questions of this sort.

Hope it helps.