How you worded that is a bit confusing, but if you have a part that is showing two different part numbers when it is used in different assemblies it is not hard to fix. Simply RMB the parts configuration name in the configurations tab, select properties, and then change the "part number displayed when used in a bill of materials" to whatever it should be. If the part number is the file name, use that. If the part number should be something else, you can either create a configuration with the appropriate part number as the name and select "Configuration Name" in the BOM options drop down, or assign different part numbers in the configuration specific custom properties and use whatever configuration description you want. You can also choose a "User Specified Name" in the configuration properties that is simply a different means to do the same exact thing as specifying different part numbers in configuration specific custom properties (i.e. Configuration Properties under the ConfigurationManager is just a different user interface).
Do note that when applying properties to the "Custom" tab within the "File Properties" that those properties apply to all configurations unless the same exact property is added to a given configuration in that configuration's "Configuration Specific" custom properties. In the latter case, the "Configuration Specific" property takes priority over the former. Get used to it though because this is a common procedure.
When I speck out something to buy I may find in on granger or msc web sights on in one of the books. I would give it a unique part # for my company and then of course I would make a drawing for that part. The drawing would speck out details and critical dims.
Then a note that says that it would meet the min requirements of said part # found at said vendor. Then purchasing agents could take the easy road and buy the one specked out or if they could get a better deal somewhere else that they know of the could get it from the company that was helping them install the new pool in their back yard. What do I care as long as it fits and it works?
Then the guy that buys the assembly from my company will call about the part failing and then we can sell them the part that they could possibly have gone down the street to the hardware store and picked up for $2.00 that we sell to him for $10.00.