Each row has an INPUT column and OUTPUT column with checkboxes. Check whether you want the metabolite to be rquired as an INPUT or as an OUTPUT. You may check both (but see below). You may check neither, in which case the metabolite is ignored.
There are three drop-down chooser at the bottom of the table. One says whether to "Or together" or "And together" the Inputs. If you choose "Or together" then any reaction with any of the metabolites selected as inputs matches. If you choose "And together," then only reactions with ALL of the metabolites checked as Input match.
There is a similar box for the output metabolites.
Finally, there is and And/Or box for combining the inputs and outputs.