Depending on whether you have added a SATA1 controller, the problems and the settings to prevent them will be different.
In my setup, the SATA1 controller is recognzied as first, this is why DiskIdxMap=0C mapped my SATA1:0 disk to the first eSata slot, which made the volume unusable for me. Setting DiskIdxMap=09 moved my SATA1:0 disk to the 10th slot, which made it usable again.
Since I have SATA0, SATA1 and the Passthrough controller, I used SataPortMap to tell DSM that each of the controller has 4 harddisks, regardless of the real number of drives.
I had 114 before, though the result was slot 1,3,4,5 have been the LSI-Harddisks, 2 was SATA0:0 and whatever DiskIdxMap inidicated was SATA1:1.
With my setup, I use DiskIdxMap=09 and SataPortMap=444. This settings work without modifiying any of the two synoinfo.conf files
Those are not the best feasable settings! DiskIdxMap determins the first disk on a controller and is a two digit hex value, while SataPortMap is a single digit value from 1-9 per controller.
I am pretty sure that DiskIdxMap=000C01 SataPortMap=114 would result in SATA1:0 = Slot1, SATA0:0 = Slot13, LSI Slot2-5.