As indicated here: http://haddock.science.uu.nl/services/HADDOCK2.2/library.html, parameters for co-factors are automatically obtained from PRODRG but they need to be labeled as HETATM in your PDB files.
If you have a large amount of similar docking runs to perform, I would advise to use the file upload interface (http://haddock.science.uu.nl/services/HADDOCK2.2/haddockserver-file.html) that allows you to directly input a HADDOCK parameter file as input instead of filling a complete form.
We do not provide, neither advise, to submit docking runs in a batch mode because of the potential high load that would be triggered on the server. However, you can either use the grid version of HADDOCK (http://milou.science.uu.nl/enmr/services/HADDOCK2.2/) or its command-line version running on your own resources, more information here: http://www.bonvinlab.org/software/haddock2.2/download/
I hope this will help you,