Strangely enough, JABBA is good at taking care of this issue. Place the ingot or dust you prefer to use into the barrel first. Any other ingot or dust of that type (copper, tin, etc.) will be changed to match the one you originally entered.
Example:
1. Put in a Thermal Expansion copper ingot into the barrel.
2. Lock the barrel.
3. Put in a stack of Engineers Toolbox copper into the barrel.
4. Pull all copper out of the barrel. It's all Thermal Expansion copper.
Example:
1. Put in a Thermal Expansion copper ingot into the barrel.
2. Lock the barrel.
3. Put in a stack of Engineers Toolbox copper into the barrel.
4. Pull all copper out of the barrel. It's all Thermal Expansion copper.