@Meydey - as @ssakunala mentioned, you can run both the BFI and LMT servers in the same BigFix environment.
After enabling the LMT site, subscribe the target LMT server host to that site. Then install and configure LMT using the Fixlets in the LMT site. Finally, follow the instructions to configure a disconnected type data source.
You can use the iSeries built-in task scheduling facility to run the disconnected scanner on a regular basis, and an NFS mount pointed at the directory defined previously for the disconnected data source as the output for the scan package.
There is no need to setup a second BigFix environment just for LMT.