Amount*ApplyMap('MappingPercentage',Code,40)/100 as PCAmount
The table MappingPercentage is a mapping table that will disappear after the load script has executed, no need to drop it. The applymap function will look up the Percentage value corresponding to the code in the mapping table. If there is no Percentage value corresponding to the code then the default value of 40 will be applied.
I'd say you could continue with loading your table 2. The mapping will just help you calculate the a new field and run a calculation. If you need to map another set of data to use in a second calculation then you simply create another mapping with similar syntax.