Hi,
are the two files from FTP are from two different countries? dont you have store/site code in the FTP file?
from store code you can define company code directly in transformation.. no need to add it to data source, just add it to target
ex: if you have store code starts with 8001, 8002...
then you can write routine something like below
if store CP 8*
company code = '800' (I am just giving a number for example)
elseif store CP 9* (for other FTP file)
company code = '900'