The partitions you chose in the earlier screen will be reformatted, despite you having formatted them using the partitioner.
While this may sound a bit crazy, there is a reason for it. The partitioner is a third party tool, called up by the installer to perform a task, then closed when its job is complete and the installer continues where it left off. The installer requires a clean environment to work with, so it must reformat all partitions before proceeding.
There is an exception for those that are reinstalling Mepis and wish to preserve their /home provided in the previous screen, which has been reported to work properly even when only 2 partitions are used, one for root (with /home included inside the root partition) and one for swap.