Support for multiple rule set is planned for release 0.14, together with thread safety.
With the current and previous releases, you can store the different rule sets in the same pyDatalog session, provided that there is no predicate name conflicts. For example, you could prefix each predicate by an identifier of the rule set it belongs too. Then, by calling the appropriate predicate, you'll activate the relevant rule set, without visible performance loss.
For prefixed predicates (referring to a python class, e.g. Employee.id[X]==Y), you would need to create python subclasses with the appropriate prefix. You could see some performance drop, but that should be small.