Okay, I just did some experimenting in a virtual machine. I started with 3 virtual disks (3 physical disks), and a optical drive, configured. All are set for SATA using AHCI. The first two disks are 2048 Mbytes, and each has a primary partition with eCS installed. The third disk is an advanced LVM drive. All are JFS.
I added a 4th virtual disk (physical). I then installed eCS. It found the drive, and allowed me to manage it, and install to it. I defined a logical volume, and formatted it as JFS. Then, the installer did it's thing, and rebooted. At reboot, it finished the install.
Note that SATA ports above 4 (starts at 0) *may* have some limitations (BIOS limits, depending on the machine), and it appears that any CD/DVD drives need to be on higher port numbers than the disks, or Air Boot won't see the disks.
So:
eCS can be installed to a third, or fourth (possibly more), physical disk, in either a primary, or logical, partition, with, or without, a primary partition present.
A disk (any size) may come with geometry that windows likes, but is invalid for eCS (that needs to be changed by eliminating the data at the front of the disk using DFSEE - I think it does 30 sectors - and let the eCS install tool fix the problem). Windows is perfectly happy with an eCS friendly geometry. Don't forget to back up anything that you may want to keep, before messing with it.
Be aware that using DFSEE under any OS other than OS/2 (eCS) can cause DFSEE to use windows friendly geometry, rather than OS/2 friendly geometry.