How to upgrade HDD to SSD and replace the optical drive with HDD

I assume you want to get the OS and apps on your SSD and the rest of your files on the HDD.

1. Attach the optical drive to it's SATA II connection and the SSD to the SATA III connection.
2. Install the OS and apps on the SSD.
3. Replace the optical drive with the HDD.

I usually place the lighter drive in the optical bay since it's not as securely connected to the body as the intended HDD slot. This also plays into the rubber shock mounts for the HDD which both protect it from accelerations as well as isolating/dampening whatever vibration the drive motors cause.

As phrased, you may get a null answer since there may not be any issues with either placement. Macs can boot from external drives and have no problems writing the sleep image to an external USB or Thunderbolt drive since the OS wants to keep the system on one drive.

The only issues I've seen are people using links to place some of the core OS and support files on a secondary drive rather than just placing user files (home folders) and safer documents on a manual/fixed tiered storage system.

With core storage and Apple's broad support of any SSD to comprise a FusionDrive the need to micromanage what files live on which tier of storage might hopefully become a thing of the past.