Assuming you have the schematic library editor running select Home | Library > Options and ensure Always Show Comment/Designator is selected.
You should now see two position indicators (asterisks). Bring up the property dialog for the designator one and uncheck Autoposition.
Your reference designators can now be manually positioned on the symbol. You can uncheck Allow Synchronization With Library to prevent placed symbols updating (this can be set on the schematic sheet per component if desired).