How to define the R-groups in the reaction scheme?

I am getting to grips with your reactor tools and am trying to define a reaction including R-groups. I have checked the documentation but cannot seem to be able to easily define an R-group list, that is the atom(s)/functional group(s) that a given R-group represents within a template molecule...I am presuming that R-groups are valid to use with the react tool?

The reaction scheme can contain R-groups. Drawing R-group queries is relatively easy with Marvin, see http://www.chemaxon.com/demosite/jchem_base/structure_search/jchem_base_r_groups/R-group.html for a Flash demonstration. However, it is not needed to draw R-groups for the reaction schemes. I think it is the best starting point to understand the usage of Reactor to start with the web based sample application at: http://www.jchem.com/examples/reactor/jsp/index.jsp. It contains some example reactions to examine. You can also find useful links to more details of the system.

Defining reactions does not require R group definition, just core atom mapping?

Exactly.