If you want to keep it separate because that's how your backup disks are then you can. Add the three backup disks one by one as Folder Destinations so you have three destinations

Then for the source disks create three backup sets for the three source drives (one each) and point each one individually at each folder. I'm not sure if the free version might limit you here, but the paid one allows more than one and just gives them the name of the driver letter. Actually backup sets might be a problem on the free version.

You don't need to do it that way apart from the fact that your backup disks aren't one contiguous disk. If it were one big disk you'd just point all three source disks at one backup destination and it would just put everything together.

Hmmm, I just looked and it looks like the free version can't do 15 minute backups anyway. It says "Once daily" vs "Continuous" and backup sets are out too. That will be an issue for separate source disks to separate backup disks.

https://www.crashplan.com/en-us/features/compare/

Sorry I guess we are so used to the paid version. Normally it wouldn't be an issue if all the disks were combined.

What are the source and destination disk sizes currently?