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Say I have a weapon on a character and Backup Bag as well. For my turn I placed a different or same weapon on the same character. But because I already have a weapon taken up does the original weapon get scrapped or can I keep both weapons and scrap Backup Bag instead?

Playing the new weapon causes the old weapon to be scrapped, but its the rules of the game that are doing this, not an effect of the new weapon. Backup Bag affects only cards such as Salvage for Parts or Grenade Launcher.
Source: Wizards of the Coast (2019-07-29)    【Link to Ruling】
Tags: Backup Bag