Medications are associated with the patient (patient → issues → medications) just as encounter records are. During an encounter a medication may be referenced as documented in encounter header. Your reference to inventory module needs some additional description to understand the basic issue here.
If you just want list of all patient medications to be included in encounter, you can check New features / improvements - #22 by mdsupport as an option.
ps
Time on this server seems to be an year behind !!!
