As chemical calculations are done by invoking Chemical Terms functions in Instant JChem you should look at the Chemical Terms manual. Here is the list of all available functions:
I give you the solution for your problem besides just giving a link to the manual. To calculate the strongest acidic/basic pKa you should use the
Please note that the number must be specified with single/double quotation marks; otherwise it works as an atom index, and it calculates the pKa of that atom. The default pKas are macroconstants.
I hope this helps,