Copy the flag table produced during the pipelining process to your data using TACOP with the TASAV file as the input (GETNAME) and the sorted multi-source data file as the output (GETONAME).
Additional flagging can be done in a number of ways. UVFLG is a non-interactive task and good for flagging whole telescopes, sources, etc. Interactive tasks include TVFLG, IBLED, EDITA and EDITR. Another option is DIFMAP as this has a superior data display capability to AIPS. However, it is possibly dangerous to export data into DIFMAP and then back into AIPS after flagging. Using DIFMAP to identify bad data which are then flagged within AIPS may be a good compromise.