Prince,
Sorry for the delayed reply as I have been very busy with some implementation issue..
Yes you have to create a new configuration in SLT.As it is a new configuration so as you need to enter that configuration in LTRC by selecting the Mass Transfer ID of your new configuration.
Logging tables & triggers will be created in Source for this configuration also.In your source system 6 triggers(INS,UPD1 & DEL) will be created per table for 2 different SLT configurations.Obviously you need to perform the initial load.
Hope this will help you now.