Change the output directory of pdflatex in TeXworks.
Go to Preferences -> Typesetting. Then select the tool you want to change in the Processing tools section. Click Edit and add the directory where the output goes by pressing + button.
NB. There is no aux directory option in pdflatex unlike latex. So the final pdf file as well as aux and log files will be in the output directory.
NB. The output directory option should be before the $fullname.
-output-directory=$directory/temp