Chad,
You have to use assembly codes, which are user-defined. When you put in the catalog info for your female plug, down toward the bottom of the dialog box are two boxes, one labeled "As main->sub", the other labeled "As sub". For the female plug, you put some code that helps you identify the sub-assembly (sometimes I use part of the sub assembly's part number), then add the catalog info for the male plug, and put the exact code in the "As sub" box. Now, when you assign the catalog number, they will be matched up. If you wish to see all of the sub-assembly numbers, there is a button to check (Sub asmb vals in pulldowns.) which is just above the Quick BOM Chk button. You can have multiple sub assemblies, as long as all the same "As sub" code.
CLear as mud???
Martin