"LVM is the best way I think, make sure to create a Volume Group (VG) that contains all your Physical Volumes (PV, i.e. your partitions), and then you can divide the VG into several Logical Volumes (LV) for your need.
LVM is not easy to grasp at first, and an image might help :
I've also seen mdadm used together with LVM. mdadm provides a software RAID system to gather the various drives. If it's to make a RAID0 system (striped disks), it might not be worth it, but it gets interesting if you want to have a RAID1 (mirror) with your two drives, and still use LVM on top of it."
As an alternative, there's a bunch of filesystems that can "merge" two filesystems into one tree. Most notable one is UnionFS, but there's also Aufs and mhddfs, last one supports some extensive features as route writing to the volume with most free space on it.
