Yes, there are two different configurations, and one is much better.
When the OS boots, there are two parts. There is a "boot sector" on a drive that is not visible to you; it's not in any partition. Then there is the partition with the OS installation. And, with Win7, there is also a 100 MB "recovery partition."
If you have a Windows OS on one drive, you attach an SSD, and you install Win7 on that SSD, the actual boot will start from the boot sector on the old drive and then use Win7 from your SSD. If you take out the old drive, the system will not boot!
In my personal opinion, you should disconnect all drives but the SSD from the system and install Win7 on the SSD. This will put the boot sector, the recovery partition, and Win7 on the same drive, and that drive will be bootable no matter what other drives are on the system.
Second best, and what Microsoft intended, is to attach the SSD and another hard drive when you install Win7, but be absolutely sure that the second drive is not bootable. No boot sector, not just no OS partition. In that case the boot segment will go on the SSD, the OS partition will go on the SSD, and the recovery partition on the other drive. This allows you to use the recovery partition if the SSD installation gets mucked up. I don't do this, myself, because I have backups of my system drive.
Strangely, the disk with the boot partition is called the "system disk," and the disk with the operating system is called the "boot disk."