if there is no matching column two flat files, that means two tables are different,no need to join the source definitions in the designer.
there is possibility to join them.
create common columns in both expression transformations.
This can be done by passing all ports to an expression transformation and then creating a output port say ID=1 in both the expression transformation of each file and then join it using a joiner on ID,hope this helps.
in mapping diagram area, double click on ur sequential file and rename the port as the other port in another sequential file.