Your config would be fine. The PERC doesn't really care about where the physical drives are on the backplane for what it does. Keeping things together is really for the human benefit. If you're concerned, the easiest thing to do would be to create a singular RAID volume for your OS, install to it, then deploy the rest of your VDs after. That would eliminate any confusion when you go to deploy your OS.  You might also consider a hotspare drive, considering the amount of drives you'd be populating the system with.
Just bought R940 and I would like to know is there any specific HDD slot occupancy order when installing HDD? I would like to setup a SQL server farm in this server and the disk slot occupancy layout will be Slot 0 & 1 - 300GB 15K (OS & SQL Program) - RAID 1 Slot 2 untill 6 - 960GB SATA (MDF Files(master, msdb, user, db) - VD01 - RAID10 Slot 14 untill 17 - 960GB SATA (LDF Files(master, msdb, user, db) - VD02 - RAID10 Slot 23 untill 24 - 480GB SATA (tempdb) - VD03 - RAID1 The subsequent vacant slot will be reserved for future VD01 and VD02 expansion. So would like to know whether this kind of setup is possible.    
R940 Hard Disk Slot Order